bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep sequencing of New World screw-worm transcripts to discover genes involved in insecticide resistance
Authors: Carvalho Renato A , Azeredo-Espin Ana Maria L , Torres Tatiana T 
Published: December 2010

AbstractBackgroundThe New World screw-worm (NWS),Cochliomyia hominivorax, is one of the most important myiasis-causing flies, causing severe losses to the livestock industry. In its current geographical distribution, this species has been controlled by the application of insecticides, mainly organophosphate (OP) compounds, but a number of lineages have been identified that are resistant to such chemicals. Despite its economic importance, only limited genetic information is available for the NWS. Here, as a part of an effort to characterize theC. hominivoraxgenome and identify putative genes involved in insecticide resistance, we sampled its transcriptome by deep sequencing of polyadenylated transcripts using the 454 sequencing technology.ResultsDeep sequencing on the 454 platform of three normalized libraries (larval, adult male and adult female) generated a total of 548,940 reads. Eighteen candidate genes coding for three metabolic detoxification enzyme families, cytochrome P450 monooxygenases, glutathione S-transferases and carboxyl/cholinesterases were selected and gene expression levels were measured using quantitative real-time polymerase chain reaction (qRT-PCR). Of the investigated candidates, only one gene was expressed differently between control and resistant larvae with, at least, a 10-fold down-regulation in the resistant larvae. The presence of mutations in the acetylcholinesterase (target site) and carboxylesterase E3 genes was investigated and all of the resistant flies presented E3 mutations previously associated with insecticide resistance.ConclusionsHere, we provided the largest database of NWS expressed sequence tags that is an important resource, not only for further studies on the molecular basis of the OP resistance in NWS fly, but also for functional and comparative studies among Calliphoridae flies. Among our candidates, only one gene was found differentially expressed in resistant individuals, and its role on insecticide resistance should be further investigated. Furthermore, the absence of mutations in the OP target site and the high frequency of mutant carboxylesterase E3 indicate that metabolic resistance mechanisms have evolved predominantly in this species.
Multiple-locus variable-number tandem repeat analysis for molecular typing of Aspergillus fumigatus
Authors: Thierry Simon , Wang Dongying , Arné Pascal , Deville Manjula , De Bruin Barbara , Nieguitsila Adélaïde , Pourcel Christine , Laroucau Karine , Chermette René , Huang Weiyi , Botterel Françoise , Guillot Jacques 
Published: December 2010

Abstract

Background
Multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) is a prominent subtyping method to resolve closely related microbial isolates to provide information for establishing genetic patterns among isolates and to investigate disease outbreaks. The usefulness of MLVA was recently demonstrated for the avian major pathogen Chlamydophila psittaci. In the present study, we developed a similar method for another pathogen of birds: the filamentous fungus Aspergillus fumigatus.

Results
We selected 10 VNTR markers located on 4 different chromosomes (1, 5, 6 and 8) of A. fumigatus. These markers were tested with 57 unrelated isolates from different hosts or their environment (53 isolates from avian species in France, China or Morocco, 3 isolates from humans collected at CHU Henri Mondor hospital in France and the reference strain CBS 144.89). The Simpson index for individual markers ranged from 0.5771 to 0.8530. A combined loci index calculated with all the markers yielded an index of 0.9994. In a second step, the panel of 10 markers was used in different epidemiological situations and tested on 277 isolates, including 62 isolates from birds in Guangxi province in China, 95 isolates collected in two duck farms in France and 120 environmental isolates from a turkey hatchery in France. A database was created with the results of the present study http://minisatellites.u-psud.fr/MLVAnet/. Three major clusters of isolates were defined by using the graphing algorithm termed Minimum Spanning Tree (MST). The first cluster comprised most of the avian isolates collected in the two duck farms in France, the second cluster comprised most of the avian isolates collected in poultry farms in China and the third one comprised most of the isolates collected in the turkey hatchery in France.

Conclusions
MLVA displayed excellent discriminatory power. The method showed a good reproducibility. MST analysis revealed an interesting clustering with a clear separation between isolates according to their geographic origin rather than their respective hosts.
Structure and expression of the maize (Zea maysL.) SUN-domain protein gene family: evidence for the existence of two divergent classes of SUN proteins in plants
Authors: Murphy Shaun P , Simmons Carl R , Bass Hank W 
Published: December 2010

AbstractBackgroundThe nuclear envelope that separates the contents of the nucleus from the cytoplasm provides a surface for chromatin attachment and organization of the cortical nucleoplasm. Proteins associated with it have been well characterized in many eukaryotes but not in plants. SUN (Sad1p/Unc-84) domain proteins reside in the inner nuclear membrane and function with other proteins to form a physical link between the nucleoskeleton and the cytoskeleton. These bridges transfer forces across the nuclear envelope and are increasingly recognized to play roles in nuclear positioning, nuclear migration, cell cycle-dependent breakdown and reformation of the nuclear envelope, telomere-led nuclear reorganization during meiosis, and karyogamy.ResultsWe found and characterized a family of maize SUN-domain proteins, starting with a screen of maize genomic sequence data. We characterized five different maizeZmSUNgenes(ZmSUN1-5), which fell into two classes (probably of ancient origin, as they are also found in other monocots, eudicots, and even mosses). The first (ZmSUN1,2), here designated canonical C-terminal SUN-domain (CCSD), includes structural homologs of the animal and fungal SUN-domain protein genes. The second (ZmSUN3, 4, 5), here designated plant-prevalent mid-SUN 3 transmembrane (PM3), includes a novel but conserved structural variant SUN-domain protein gene class. Mircroarray-based expression analyses revealed an intriguing pollen-preferred expression forZmSUN5mRNA but low-level expression (50-200 parts per ten million) in multiple tissues for all the others. Cloning and characterization of a full-length cDNA for a PM3-type maize gene,ZmSUN4, is described. Peptide antibodies to ZmSUN3, 4 were used in western-blot and cell-staining assays to show that they are expressed and show concentrated staining at the nuclear periphery.ConclusionsThe maize genome encodes and expresses at least five different SUN-domain proteins, of which the PM3 subfamily may represent a novel class of proteins with possible new and intriguing roles within the plant nuclear envelope. Expression levels forZmSUN1-4 are consistent with basic cellular functions, whereasZmSUN5 expression levels indicate a role in pollen. Models for possible topological arrangements of the CCSD-type and PM3-type SUN-domain proteins are presented.
Administration of a Tropomyosin Receptor Kinase Inhibitor Attenuates Sarcoma-Induced Nerve Sprouting, Neuroma Formation and Bone Cancer Pain
Authors: Ghilardi Joseph R , Freeman Katie T , Jimenez-Andrade Juan M , Mantyh William G , Bloom Aaron P , Kuskowski Michael A , Mantyh Patrick W 
Published: December 2010

Pain often accompanies cancer and most current therapies for treating cancer pain have significant unwanted side effects. Targeting nerve growth factor (NGF) or its cognate receptor tropomyosin receptor kinase A (TrkA) has become an attractive target for attenuating chronic pain. In the present report, we use a mouse model of bone cancer pain and examine whether oral administration of a selective small molecule Trk inhibitor (ARRY-470, which blocks TrkA, TrkB and TrkC kinase activity at low nm concentrations) has a significant effect on cancer-induced pain behaviors, tumor-induced remodeling of sensory nerve fibers, tumor growth and tumor-induced bone remodeling. Early/sustained (initiated day 6 post cancer cell injection), but not late/acute (initiated day 18 post cancer cell injection) administration of ARRY-470 markedly attenuated bone cancer pain and significantly blocked the ectopic sprouting of sensory nerve fibers and the formation of neuroma-like structures in the tumor bearing bone, but did not have a significant effect on tumor growth or bone remodeling. These data suggest that, like therapies that target the cancer itself, the earlier that the blockade of TrkA occurs, the more effective the control of cancer pain and the tumor-induced remodeling of sensory nerve fibers. Developing targeted therapies that relieve cancer pain without the side effects of current analgesics has the potential to significantly improve the quality of life and functional status of cancer patients.
Anterior cruciate ligament repair with LARS (ligament advanced reinforcement system): a systematic review
Authors: Machotka Zuzana , Scarborough Ian , Duncan Will , Kumar Saravana , Perraton Luke 
Published: December 2010

Abstract

Background
Injury to the anterior cruciate ligament (ACL) of the knee is common. Following complete rupture of the ACL, insufficient re-vascularization of the ligament prevents it from healing completely, creating a need for reconstruction. A variety of grafts are available for use in ACL reconstruction surgery, including synthetic grafts. Over the last two decades new types of synthetic ligaments have been developed. One of these synthetic ligaments, the Ligament Advanced Reinforcement System (LARS), has recently gained popularity.
The aim of this systematic review was to assess the current best available evidence for the effectiveness of the LARS as a surgical option for symptomatic, anterior cruciate ligament rupture in terms of graft stability, rehabilitation time and return to pre-injury function.

Method
This systematic review included studies using subjects with symptomatic, ACL ruptures undergoing LARS reconstruction. A range of electronic databases were searched in May 2010. The methodological quality of studies was appraised with a modified version of the Law critical appraisal tool. Data relating to study characteristics, surgical times, complication rates, outcomes related to knee stability, quality of life, function, and return to sport as well as details of rehabilitation programs and timeframes were collected.

Results
This review identified four studies of various designs, of a moderate methodological quality. Only one case of knee synovitis was reported. Patient satisfaction with LARS was high. Graft stability outcomes were found to be inconsistent both at post operative and at follow up periods. The time frames of rehabilitation periods were poorly reported and at times omitted. Return to pre-injury function and activity was often discussed but not reported in results.

Conclusions
There is an emerging body of evidence for LARS with comparable complication rates to traditional surgical techniques, and high patient satisfaction scores. However, this systematic review has highlighted several important gaps in the existing literature that require future prospective investigation. The findings of this review were equivocal with regards to other measures such as graft stability and long term functional outcomes. While the importance of rehabilitation following LARS is well recognised, there is limited evidence to guide rehabilitation protocols.
Risk factors for ductal and lobular breast cancer: results from the nurses' health study
Authors: Kotsopoulos Joanne , Chen Wendy Y , Gates Margaret A , Tworoger Shelley S , Hankinson Susan E , Rosner Bernard A 
Published: December 2010

Abstract
Introduction
Ductal and lobular carcinomas are the two most common types of invasive breast cancer. Whether well-established risk factors are differentially associated with risk on the basis of histologic subtype is not clear. We prospectively investigated the association between a number of hormonal and nonhormonal exposures and risk defined by histologic subtype among 4,655 ductal and 659 lobular cases of postmenopausal breast cancer from the Nurses' Health Study.

Methods
Multivariate Cox proportional hazards regression stratified by histologic subtype and time period was used to examine the association between risk factors and the incidence of ductal and lobular subtypes. For each exposure, we calculated the P value for heterogeneity using a likelihood ratio test comparing models with separate estimates for the two subtypes versus a single estimate across subtypes.

Results
The associations with age at menarche (P-heterogeneity (het) = 0.03), age at first birth (P-het < 0.001) and postmenopausal hormone use (P-het < 0.001) were more strongly associated with lobular cancers. The associations with age, nulliparity, parity, age at menopause, type of menopause, alcohol intake, adult body mass index (BMI), BMI at age 18, family history of breast cancer and personal history of benign breast disease did not vary by subtype (P-het ≥ 0.08). Results were similar when we restricted the analyses to estrogen receptor-positive and progesterone receptor-positive tumors.

Conclusions
These data indicate that breast cancer is a heterogeneous disease, and the differential association with a number of risk factors is suggestive of etiologically distinct tumors. Epidemiological analyses should continue to take into account a modifying role of histology.
Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition
Authors: Adey Andrew , Morrison Hilary G , Asan  , Xun Xu , Kitzman Jacob O , Turner Emily H , Stackhouse Bethany , MacKenzie Alexandra P , Caruccio Nicholas C , Zhang Xiuqing , Shendure Jay 
Published: December 2010

AbstractWe characterize and extend a highly efficient method for constructing shotgun fragment libraries in which transposase catalyzes in vitro DNA fragmentation and adaptor incorporation simultaneously. We apply this method to sequencing a human genome and find that coverage biases are comparable to those of conventional protocols. We also extend its capabilities by developing protocols for sub-nanogram library construction, exome capture from 50 ng of input DNA, PCR-free and colony PCR library construction, and 96-plex sample indexing.
Directional escape behavior in allis shad (Alosa alosa) exposed to ultrasonic clicks mimicking an approaching toothed whale
Authors: Wilson Maria , Schack Henriette B. , Madsen Peter Teglberg , Surlykke Annemarie , Wahlberg Magnus 
Published: December 2010

SUMMARYToothed whales emit high-powered ultrasonic clicks to echolocate a wide range of prey. It may be hypothesized that some of their prey species have evolved capabilities to detect and respond to such ultrasonic pulses in a way that reduces predation, akin to the situation for many nocturnal insects and echolocating bats. Using high-speed film recordings and controlled exposures, we obtained behavioural evidence that simulated toothed whale biosonar clicks elicit highly directional anti-predator responses in an ultrasound-sensitive allis shad (Alosa alosa). Ten shad were exposed to 192 dB re. 1 μPa (pp) clicks centred at 40 kHz at repetition rates of 1, 20, 50 and 250 clicks s–1 with summed energy flux density levels of 148, 161, 165 and 172 dB re. 1 μPa2 s. The exposures mimicked the acoustic exposure from a delphinid toothed whale in different phases of prey search and capture. The response times of allis shad were faster for higher repetition rates of clicks with the same sound pressure level. None of the fish responded to a single click, but had median response times of 182, 93 and 57 ms when exposed to click rates of 20, 50 and 250 clicks s–1, respectively. This suggests that the ultrasound detector of allis shad is an energy detector and that shad respond faster when exposed to a nearby fast-clicking toothed whale than to a slow-clicking toothed whale far away. The findings are thus consistent with the hypothesis that shad ultrasound detection is used for reducing predation from echolocating toothed whales.
Intraspecific scaling of chewing cycle duration in three species of domestic ungulates
Authors: Stover Kristin K. , Williams Susan H. 
Published: December 2010

SUMMARY
In mammals, chewing cycle duration (CCD) increases with various measures of size, scaling with body mass0.13–0.28 and jaw length0.55. Proposed explanations for these scaling relationships include the allometry of body size, basal metabolic rate and tooth size, on the one hand, and pendular mechanics treating the jaw as a gravity-driven pendulum, on the other. Little is known, however, about the relationship between CCD and size within species. Recent research in dogs demonstrates altogether different scaling exponents and weaker correlations. This research suggests that breed-specific growth rates influence the maturation of the neural networks generating chewing rhythm, which may be altered because of changes in jaw mass during early postnatal growth. Here, we explored the intraspecific scaling of CCD within a sample of adult horses ranging from miniatures to draft breeds and an ontogenetic sample of goats and alpacas from infants to adults. In horses, CCD scales with body mass0.19 and jaw length0.57, although in neither case is the correlation significant. In the ontogenetic samples of goats and alpacas, CCD is significantly correlated with body mass, scaling as CCD∝body mass0.37 in both species. In goats, but not alpacas, CCD is also significantly correlated with jaw length, scaling as jaw length1.032. As in dogs, the scaling of CCD in horses may reflect the influence of selective breeding on growth trajectories of different breeds, resulting in reduced body and jaw size differences among infants, when CCD is established, compared with adults. However, the allometric scaling of tooth size in horses of different breeds may be a potential influence on the scaling of CCD. The scaling of CCD with body and jaw size in goats, and to a lesser extent in alpacas, also suggests that the development of peripheral masticatory structures such as the teeth and occlusal relations may play a role in changes in CCD during the earliest stages of postnatal ontogeny.
A diverse family of novel peptide toxins from an unusual cone snail, Conus californicus
Authors: Gilly W. F. , Richmond T. A. , Duda T. F. , Elliger C. , Lebaric Z. , Schulz J. , Bingham J. P. , Sweedler J. V. 
Published: December 2010

SUMMARY
Diversity among Conus toxins mirrors the high species diversity in the Indo-Pacific region, and evolution of both is thought to stem from feeding-niche specialization derived from intra-generic competition. This study focuses on Conus californicus, a phylogenetic outlier endemic to the temperate northeast Pacific. Essentially free of congeneric competitors, it preys on a wider variety of organisms than any other cone snail. Using molecular cloning of cDNAs and mass spectrometry, we examined peptides isolated from venom ducts to elucidate the sequences and post-translational modifications of two eight-cysteine toxins (cal12a and cal12b of type 12 framework) that block voltage-gated Na+ channels. Based on homology of leader sequence and mode of action, these toxins are related to the O-superfamily, but differ significantly from other members of that group. Six of the eight cysteine residues constitute the canonical framework of O-members, but two additional cysteine residues in the N-terminal region define an O+2 classification within the O-superfamily. Fifteen putative variants of Cal12.1 toxins have been identified by mRNAs that differ primarily in two short hypervariable regions and have been grouped into three subtypes (Cal12.1.1–3). This unique modular variation has not been described for other Conus toxins and suggests recombination as a diversity-generating mechanism. We propose that these toxin isoforms show specificity for similar molecular targets (Na+ channels) in the many species preyed on by C. californicus and that individualistic utilization of specific toxin isoforms may involve control of gene expression.
The influence of drinking water on the δD and δ18O values of house sparrow plasma, blood and feathers
Authors: Wolf Nathan , Bowen Gabriel J. , del Rio Carlos Martinez 
Published: December 2010

SUMMARY
We investigated the relationships between the δdeuterium (δD) and the δ18oxygen (δ18O) of drinking water and the δD and δ18O of blood plasma, red blood cells and feathers in house sparrows (Passer domesticus) fed on diets with identical hydrogen and oxygen isotopic compositions and five isotopically distinct drinking water treatments. We expected and, with only one exception (18O in blood plasma), found linear relationships between the δD and δ18O values of drinking water and those of bird tissues. The slopes of these relationships, which estimate the percentage contributions of drinking water to the tissue isotopic signatures, were lower than those of previous studies. We found significant differences in the δD and δ18O values of feathers, red blood cells and plasma solids. In feathers and red blood cells, δD and δ18O values were linearly correlated. Our results have three implications for isotopic field studies: (1) if the isotopic composition of drinking water differs from that of food, its effect on tissue isotope values can confound the assignment of animals to a site of origin; (2) comparisons of the δD and δ18O values of different tissues must account for inter-tissue discrimination factors; and (3) δD/δ18O linear relationships are probably as prevalent in animal systems as they are in geohydrological systems. These relationships may prove to be useful tools in animal isotopic ecology.
Foreign genes and novel hydrophilic protein genes participate in the desiccation response of the bdelloid rotifer Adineta ricciae
Authors: Boschetti Chiara , Pouchkina-Stantcheva Natalia , Hoffmann Pia , Tunnacliffe Alan 
Published: December 2010

SUMMARY
Bdelloid rotifers are aquatic micro-invertebrates with the ability to survive extreme desiccation, or anhydrobiosis, at any life stage. To gain insight into the molecular mechanisms used by bdelloids during anhydrobiosis, we constructed a cDNA library enriched for genes that are upregulated in Adineta ricciae 24 h after onset of dehydration. Resulting expressed sequence tags (ESTs) were analysed and sequences grouped into categories according to their probable identity. Of 75 unique sequences, approximately half (36) were similar to known genes from other species. These included genes encoding an unusual group 3 late embryogenesis abundant protein, and a number of other stress-related and DNA repair proteins. Open reading frames from a further 39 novel sequences, without counterparts in the database, were screened for the characteristics of intrinsically disordered proteins, i.e. hydrophilicity and lack of stable secondary structure. Such proteins have been implicated in desiccation tolerance and at least five were found. The majority of the genes identified was confirmed by real-time quantitative PCR to be capable of upregulation in response to evaporative water loss. Remarkably, further database and phylogenetic analysis highlighted four ESTs that are present in the A. ricciae genome but which represent genes probably arising from fungi or bacteria by horizontal gene transfer. Therefore, not only can bdelloid rotifers accumulate foreign genes and render them transcriptionally competent, but their expression pattern can be modified for participation in the desiccation stress response, and is presumably adaptive in this context.