bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative Microbial Community Analysis of Three Different Sulfidic Mine Tailing Dumps Generating Acid Mine Drainage
Authors: Kock Dagmar , Schippers Axel 
Published: June 2008

ABSTRACT

The microbial communities of three different sulfidic and acidic mine waste tailing dumps located in Botswana, Germany, and Sweden were quantitatively analyzed using quantitative real-time PCR (Q-PCR), fluorescence in situ hybridization (FISH), catalyzed reporter deposition-FISH (CARD-FISH), Sybr green II direct counting, and the most probable number (MPN) cultivation technique. Depth profiles of cell numbers showed that the compositions of the microbial communities are greatly different at the three sites and also strongly varied between zones of oxidized and unoxidized tailings. Maximum cell numbers of up to 10
9
cells g
−1
dry weight were determined in the pyrite or pyrrhotite oxidation zones, whereas cell numbers in unoxidized tailings were significantly lower.
Bacteria
dominated over
Archaea
and
Eukarya
at all tailing sites. The acidophilic Fe(II)- and/or sulfur-oxidizing
Acidithiobacillus
spp. dominated over the acidophilic Fe(II)-oxidizing
Leptospirillum
spp. among the
Bacteria
at two sites. The two genera were equally abundant at the third site. The acidophilic Fe(II)- and sulfur-oxidizing
Sulfobacillus
spp. were generally less abundant. The acidophilic Fe(III)-reducing
Acidiphilium
spp. could be found at only one site. The neutrophilic Fe(III)-reducing
Geobacteraceae
as well as the
dsrA
gene of sulfate reducers were quantifiable at all three sites. FISH analysis provided reliable data only for tailing zones with high microbial activity, whereas CARD-FISH, Q-PCR, Sybr green II staining, and MPN were suitable methods for a quantitative microbial community analysis of tailings in general.
Molecular Epidemiology of
Campylobacter jejuni
Populations in Dairy Cattle, Wildlife, and the Environment in a Farmland Area
Authors: Kwan Patrick S. L. , Barrigas Mishele , Bolton Frederick J. , French Nigel P. , Gowland Peter , Kemp Richard , Leatherbarrow Howard , Upton Mathew , Fox Andrew J. 
Published: June 2008

ABSTRACT

We describe a cross-sectional study of the molecular epidemiology of
Campylobacter jejuni
in a dairy farmland environment, with the aim of elucidating the dynamics of horizontal transmission of
C. jejuni
genotypes among sources in the area. A collection of 327
C. jejuni
isolates from cattle, wildlife, and environmental sources in a 100-km
2
area of farmland in northwest England was characterized by multilocus sequence typing. A total of 91 sequence types and 18 clonal complexes were identified. Clonal complexes ST-21, ST-45, and ST-61, which have been frequently associated with human disease, were the most commonly recovered genotypes in this study. In addition, widely distributed genotypes as well as potentially host-associated genotypes have been identified, which suggests that both restricted and interconnecting pathways of transmission may be operating in the dairy farmland environment. In particular, the ST-61 complex and the ST-21 complex were significantly associated with cattle. In contrast, complex strains ST-45, ST-952, and ST-677 were isolated predominantly from wild birds, wild rabbits, and environmental water. A considerable number of novel sequence types have also been identified, which were unassigned to existing clonal complexes and were frequently isolated from wildlife and environmental sources. The segregated distribution of genotypes among samples from different sources suggests that their transmission to humans is perhaps via independent routes. Insight into the dynamics and interactions of
C. jejuni
populations between important animal reservoirs and their surrounding environment would improve the identification of sources of
Campylobacter
infection and the design of control strategies.
A Thioredoxin Family Protein of the Apicoplast Periphery Identifies Abundant Candidate Transport Vesicles in
Toxoplasma gondii
Authors: DeRocher Amy E. , Coppens Isabelle , Karnataki Anuradha , Gilbert Luke A. , Rome Michael E. , Feagin Jean E. , Bradley Peter J. , Parsons Marilyn 
Published: June 2008

ABSTRACT

Toxoplasma gondii
, which causes toxoplasmic encephalitis and birth defects, contains an essential chloroplast-related organelle to which proteins are trafficked via the secretory system. This organelle, the apicoplast, is bounded by multiple membranes. In this report we identify a novel apicoplast-associated thioredoxin family protein, ATrx1, which is predominantly soluble or peripherally associated with membranes, and which localizes primarily to the outer compartments of the organelle. As such, it represents the first protein to be identified as residing in the apicoplast intermembrane spaces. ATrx1 lacks the apicoplast targeting sequences typical of luminal proteins. However, sequences near the N terminus are required for proper targeting of ATrx1, which is proteolytically processed from a larger precursor to multiple smaller forms. This protein reveals a population of vesicles, hitherto unrecognized as being highly abundant in the cell, which may serve to transport proteins to the apicoplast.
Septins Stabilize Mitochondria in
Tetrahymena thermophila
Authors: Włoga D. , Strzyżewska-Jówko I. , Gaertig J. , Jerka-Dziadosz M. 
Published: June 2008

ABSTRACT

We describe phylogenetic and functional studies of three septins in the free-living ciliate
Tetrahymena thermophila
. Both deletion and overproduction of septins led to vacuolization of mitochondria, destabilization of the nuclear envelope, and increased autophagy. All three green fluorescent protein-tagged septins localized to mitochondria. Specific septins localized to the outer mitochondrial membrane, to septa formed during mitochondrial scission, or to the mitochondrion-associated endoplasmic reticulum. The only other septins known to localize to mitochondria are human ARTS and murine M-septin, both alternatively spliced forms of Sep4 (S. Larisch, Cell Cycle 3:1021-1023, 2004; S. Takahashi, R. Inatome, H. Yamamura, and S. Yanagi, Genes Cells 8:81-93, 2003). It therefore appears that septins have been recruited to mitochondrial functions independently in at least two eukaryotic lineages and in both cases are involved in apoptotic events.
Bias between the Left and Right Inverted Repeats during IS911Targeted Insertion
Authors: Rousseau P. , Loot C. , Turlan C. , Nolivos S. , Chandler M. 
Published: June 2008

ABSTRACTIS911is a bacterial insertion sequence composed of two consecutive overlapping open reading frames (ORFs [orfAandorfB]) encoding the transposase (OrfAB) as well as a regulatory protein (OrfA). These ORFs are bordered by terminal left and right inverted repeats (IRL and IRR, respectively) with several differences in nucleotide sequence. IS911transposition is asymmetric: each end is cleaved on one strand to generate a free 3′-OH, which is then used as the nucleophile in attacking the opposite insertion sequence (IS) end to generate a free IS circle. This will be inserted into a new target site. We show here that the ends exhibit functional differences which, in vivo, may favor the use of one compared to the other during transposition. Electromobility shift assays showed that a truncated form of the transposase [OrfAB(1-149)] exhibits higher affinity for IRR than for IRL. While there was no detectable difference in IR activities during the early steps of transposition, IRR was more efficient during the final insertion steps. We show here that the differential activities between the two IRs correlate with the different affinities of OrfAB(1-149) for the IRs during assembly of the nucleoprotein complexes leading to transposition. We conclude that the two inverted repeats are not equivalent during IS911transposition and that this asymmetry may intervene to determine the ordered assembly of the different protein-DNA complexes involved in the reaction.
Complete Genome Sequence of
Neisseria gonorrhoeae
NCCP11945
Authors: Chung Gyung Tae , Yoo Jeong Sik , Oh Hee Bok , Lee Yeong Seon , Cha Sun Ho , Kim Sang Jun , Yoo Cheon Kwon 
Published: June 2008

ABSTRACT

Neisseria gonorrhoeae
is an obligate human pathogen that is the etiological agent of gonorrhea. We explored variations in the genes of a multidrug-resistant
N. gonorrhoeae
isolate from a Korean patient in an effort to understand the prevalence, antibiotic resistance, and importance of horizontal gene transfer within this important, naturally competent organism. Here, we report the complete annotated genome sequence of
N. gonorrhoeae
strain NCCP11945.
Effects on Translation Pausing of Alterations in Protein and RNA Components of the Ribosome Exit Tunnel
Authors: Lawrence Marlon G. , Lindahl Lasse , Zengel Janice M. 
Published: June 2008

ABSTRACT

Amino acids are polymerized into peptides in the peptidyl transferase center of the ribosome. The nascent peptides then pass through the exit tunnel before they reach the extraribosomal environment. A number of nascent peptides interact with the exit tunnel and stall elongation at specific sites within their peptide chain. Several mutational changes in RNA and protein components of the ribosome have previously been shown to interfere with pausing. These changes are localized in the narrowest region of the tunnel, near a constriction formed by ribosomal proteins L4 and L22. To expand our knowledge about peptide-induced pausing, we performed a comparative study of pausing induced by two peptides, SecM and a short peptide, Crb
CmlA
, that requires chloramphenicol as a coinducer of pausing. We analyzed the effects of 15 mutational changes in L4 and L22, as well as the effects of methylating nucleotide A2058 of 23S rRNA, a nucleotide previously implicated in pausing and located close to the L4-L22 constriction. Our results show that methylation of A2058 and most mutational changes in L4 and L22 have differential effects on pausing in response to Crb
CmlA
and SecM. Only one change, a 6-amino-acid insertion after amino acid 72 in L4, affects pausing in both peptides. We conclude that the two peptides interact with different regions of the exit tunnel. Our results suggest that either the two peptides use different mechanisms of pausing or they interact differently but induce similar inhibitory conformational changes in functionally important regions of the ribosome.
Subtyping of Avian Influenza Viruses H1 to H15 on the Basis of Hemagglutinin Genes by PCR Assay and Molecular Determination of Pathogenic Potential
Authors: Tsukamoto Kenji , Ashizawa Hisayoshi , Nakanishi Koji , Kaji Noriyuki , Suzuki Kotaro , Okamatsu Masatoshi , Yamaguchi Shigeo , Mase Masaji 
Published: July 2008

ABSTRACT
Serious concern about the worldwide transmission of the Asian H5N1 highly pathogenic (HP) avian influenza (AI) virus by migratory birds surrounds the importance of the AI global surveillance in wild aquatic birds and underscores the requirement for a reliable subtyping method of AI viruses. PCR is advantageous due to its simplicity, lower cross-reactivity, and unlimited reagent supply. Currently, the only available hemagglutinin (HA) subtyping primer set that can subtype H1 through H15 is not fully evaluated and, since it only targets HA1, is unavailable for molecular pathotyping of AI viruses. Our preliminary experiments found that these primer sets were cross-reactive and missed some recent AI viruses. In this study, we developed new primer sets against HA cleavage sites for subtyping H1 to H15 genes and for molecular pathotyping. Our primer sets were subtype specific and detected 99% of previously identified HA genes (115/116, 1949 to March 2006), and the correct amplifications of HA genes were confirmed by sequence analyses of all 115 PCR products. The primer sets successfully subtyped most of the recent AI viruses isolated in Japan (96% [101/105], October 2006 to March 2007). Taken together, our primer sets could efficiently detect HA genes (98% [216/221]) of both previously and recently identified HA genes or of both American (29/29) and Eurasian (187/192) lineages. All 38 H5 and 13 H7 viruses were molecularly pathotyped by sequencing analyses of the HA cleavage site. In contrast, despite efficient detection of previously identified strains (98% [114/116]), the published primer sets exhibited lower specificity and lower detection efficiency against recent AI viruses (80% [84 of 105]). These results indicate that our primers are useful not only for HA subtyping but also for molecular pathotyping of both previous and recent AI viruses. These advancements will enable general diagnostic laboratories to subtype AI viruses for the surveillance in wild aquatic birds.
Mapping of the CXCR4 Binding Site within Variable Region 3 of the Feline Immunodeficiency Virus Surface Glycoprotein
Authors: Sundstrom Magnus , White Rebecca L. , de Parseval Aymeric , Sastry K. Jagannadha , Morris Garrett , Grant Chris K. , Elder John H. 
Published: July 2008

ABSTRACT

Feline immunodeficiency virus (FIV) shares with T-cell tropic strains of human immunodeficiency virus type 1 (HIV-1) the use of the chemokine receptor CXCR4 for cellular entry. In order to map the interaction of the FIV envelope surface unit (SU) with CXCR4, full-length FIV SU-Fc as well as constructs with deletions of extended loop L2, V3, V4, or V5 were produced in stable CHO cell lines. Binding studies were performed using these proteins on 3201 cells (CXCR4
hi
CD134
−
), with or without the CXCR4 inhibitor AMD3100. The findings established that SU binding to CXCR4 specifically requires the V3 region of SU. Synthetic peptides spanning the V3 region as well as a panel of monoclonal antibodies (MAbs) to SU were used to further map the site of CXCR4 interaction. Both the SU V3-specific antibodies and the full-length V3 peptide potently blocked binding of SU to CXCR4 and virus entry. By using a set of nested peptides overlapping a region of SU specifically recognized by CD134-dependent neutralizing V3 MAbs, we showed that the neutralizing epitope and the region required for CXCR4 binding are within the same contiguous nine-amino-acid sequence of V3. Site-directed mutagenesis was used to reveal that serine 393 and tryptophan 394 at the predicted tip of V3 are required to facilitate entry into the target cell via CXCR4. Although the amino acid sequences are not identical between FIV and HIV, the ability of FIV to bind and utilize both feline and human CXCR4 makes the feline model an attractive venue for development of broad-based entry antagonists.
Low-pH-Induced Membrane Fusion Mediated by Human Metapneumovirus F Protein Is a Rare, Strain-Dependent Phenomenon
Authors: Herfst Sander , Mas Vicente , Ver Lorena S. , Wierda Rutger J. , Osterhaus Albert D. M. E. , Fouchier Ron A. M. , Melero José A. 
Published: July 2008

ABSTRACT
Membrane fusion promoted by human metapneumovirus (HMPV) fusion (F) protein was suggested to require low pH (R. M. Schowalter, S. E. Smith, and R. E. Dutch, J. Virol. 80:10931-10941, 2006). Using prototype F proteins representing the four HMPV genetic lineages, we detected low-pH-dependent fusion only with some lineage A proteins and not with lineage B proteins. A glycine at position 294 was found responsible for the low-pH requirement in lineage A proteins. Only 6% of all HMPV lineage A F sequences have 294G, and none of the lineage B sequences have 294G. Thus, acidic pH is not a general trigger of HMPV F proteins for activity.
A Careful Management: The Borghese Family and their Fiefs in Early Modern Lazio
Authors: Forclaz Bertrand 
Published: July 2008

AbstractThis article investigates economic management of fiefs as well as social relationships between lords and vassals in 17th- and 18th-century central Italy. Up to recent years, historians of early modern Italy as well as other European countries have stressed the “archaic” features of noble management, which would have prevented the emergence of a “modern” market-oriented agrarian economy, or have portrayed noblemen as market-oriented landowners neglecting their seigneurial rights. I argue here that both dimensions were present in noble management, as lords did not choose between them, but rather leaned upon one or the other according to circumstances. I base my argument on the case of the Borghese, one of the wealthiest papal families of the 17th century. Finally, this study shows that modern elements could be brought into a model characterized by strong seigneurial rights.
The Conservation of Nature Under the T'Ang Dynasty
Authors: Schafer Edward H. 
Published: July 2008

AbstractThe study of the history of man's knowledge of plants and animals is all the more necessary in that it has been neglected in favor of the study of the development of tools. For instance, as Lewis Mumford has pointed out 1), knowledge of the modes of reproduction and growth of plants was more necessary to the development of agriculture in Neolithic times than was the invention of such tools as the spade, the hoe, and the plow, around which most conventional notions of "technological history" revolve. In presenting a paper, then, on attitudes towards the preservation of living things and their habitat in medieval China, I hope to redress the balance of interest, if only slightly, in favor of man's direct involvement with the natural world, and away from study of artifacts preserved in museums. It is, of course, necessary to do this through the study of documents. This paper is divided into two parts. In the first I will discuss some cultural factors which seem to have influenced policy relating to the conservation of nature, and in the second I will discuss some of the particular measures undertaken to make policy effective.
Notice sur Jean Thenaud
Authors: Engels J. 
Published: June 2008

AbstractDans la Notice bibliographique sur Pierre BersuireI, j'ai signalé2 que le frère mineur Jean Thenaud avait consacré à cet auteur un passage de sa Margarite de France, mais le temps m'avait manqué pour le retracer. Puis, Thenaud s'étant lui aussi occupé de mythologie, la question se posait tout naturellement de savoir dans quelle mesure il a été tributaire de l'Ovidius moralizatus de Bersuire. Je livre ici le résultat de recherches assez complexes, car la bibliographie de Thenaud s'est révélée des plus embrouillées.
Social Dominance and Territoriality in the Bicolor Damselfish, e uPomacentr Us Par Ti t uS (Poey) (Pisces : Pomacentridae)
Authors: Myrberg Arthur A. 
Published: June 2008

AbstractThe social organization of two comparable colonies of bicolor damselfish, Eupomacentrus partius (Poey), is described at various times of the year. A small laboratory colony (8 adults) was observed during two different social phases. The first included the initial establishment of dominant-subordinate relationships among its members, as well as the establishment of the general spatial distribution of fish within the aquarium. The second phase was characterized hy a high level of territoriality and reproductive activity. A field colony of similar size (9 adults, 4 juveniles) was observed by SCUBA and underwater television also during the reproductive phase. This colony was located 1.5 km off the west coast of North Bimini, Bahamas and at a depth of 20 m. The social structure of both colonies was characterized by a straight-line, nip-dominant hierarchy which was stable and largely size-dependent. Aggressiveness and maleness also appeared to play important roles in the dominance relationships. Differences in the distribution of chases and challenges recorded from the laboratory colony during the two differing social phases indicated that dynamic processes were underlying the basic social structure of both colonies. Little or no diurnal fluctuation in aggressiveness was apparent during the two phases studied in the laboratory. The level of chasing activity throughout the day, however, was well correlated with hierarchical rank during the initial phase of observations, but such was not the case during the later phase. The initial phase was also characterized by closely ranked individuals directing most "attention" at one another, while during the later reproductive phase, much of this "attention" was directed at the Omega fish. It appeared as if the Omega was playing the role of a "scapegoat" for the directed aggression of higher ranking members and thereby relieving aggressive tension among those members of the colony. A similar phenomenon, operating in the field colony, was also indicated by limited data. The important role of prior residence within a colony and within a specific area is illustrated by examples from the field. Finally, evidence is brought forth to suggest that interspecific aggression. although seldom studied, is a most important factor in the lives and habits of animals living within the reef community.
Reproductive Behaviour of Sepsis Cynipsea (L.) (Diptera: Sepsidae) Ii. the Significance of the Precopulatory Passive Phase and Emigration
Authors: Parker G.A. 
Published: June 2008

AbstractThe passive phase of Sepsis cynipsea (L.) differs from that of Scatophaga stercoraria L. in that it is pre-, not postcopulatory, though both appear to have evolved through intra-male competition. Male S. cynipsea which 'established a claim' to females for a possible eventual copulation would have had a high selective advantage over males which waited until females had finished oviposition before mounting. The most advantageous male strategy would, however, be a postcopulatory passive phase of the Scatophaga type. Unlike Scatophaga, the female rejection reactions in S. cynipsea are highly effective in preventing copulation; though they frequently fail to prevent mounting. For this reason, and because the precopulatory passive phase is advantageous to the female in avoiding rejection delay during oviposition, the nett result of intrasexual selection should stabilize at a precopulatory passive phase. This is providing that at least some of the females guarded during oviposition will afterwards mate. Emigration from the dung to the surrounding grass after oviposition is effected by the female. This behaviour reduces the rates of attack and 'take-over' (where the original male is displaced by another male), but because copula duration is related to temperature and the dung is hotter than the surrounding grass, there would be a nett time gain in staying on the dropping. The adaptive significance of emigration may be to reduce exposure to predation, the chances of which appear to be much higher on the dung than in the grass.
Experience and Selection Behavior in the Food Habits of Peromyscus: Use of Olfaction
Authors: Drickamer Lee C. 
Published: June 2008

AbstractFeeding behavior in young and adult Peromyscus maniculalus and P. lcucopus was studied by examining the extent to which food habit could be modified by prior experience and by decribing the pattern of feeding behavior used by the mice in a three-choice situation. Modifiability of food preferences was investigated by providing mice with specific food-cue experience and testing their subsequent preferences. The food preferences of young and adult P. leucopus and young P. m. baiudi were significantly affected by the food-cue conditioning and the effect persisted for at least 30 days. Adult P. m. bairdi food preferences were not affected by the prior experience. Automatic monitoring devices were used to describe the patterning of feeding behavior with three choices present. Analyses showed that; (1) young mice were less flexible initially than adult mice; (2) adult P. leucopus switched feeding sites more frequently than any other group; and (3) young P. m. bairdi avoided a novel food-cue stimulus whereas the other test groups ate readily from this source. The principal conclusion was that P. leucopus exhibited more flexibility in feeding behavior than P. m. bairdi. Food habits and flexibility of feeding behavior were discussed in relation to the habitat distributions of these two species of mice.