bluuebunny/crossref_metadata_2025 huggingface dataset:
Disentangling the effects of forage, social rank, and risk on movement autocorrelation of elephants using Fourier and wavelet analyses
Authors: Wittemyer George , Polansky Leo , Douglas-Hamilton Iain , Getz Wayne M.
Published: December 2008

The internal state of an individual—as it relates to thirst, hunger, fear, or reproductive drive—can be inferred by referencing points on its movement path to external environmental and sociological variables. Using time-series approaches to characterize autocorrelative properties of step-length movements collated every 3 h for seven free-ranging African elephants, we examined the influence of social rank, predation risk, and seasonal variation in resource abundance on periodic properties of movement. The frequency domain methods of Fourier and wavelet analyses provide compact summaries of temporal autocorrelation and show both strong diurnal and seasonal based periodicities in the step-length time series. This autocorrelation is weaker during the wet season, indicating random movements are more common when ecological conditions are good. Periodograms of socially dominant individuals are consistent across seasons, whereas subordinate individuals show distinct differences diverging from that of dominants during the dry season. We link temporally localized statistical properties of movement to landscape features and find that diurnal movement correlation is more common within protected wildlife areas, and multiday movement correlations found among lower ranked individuals are typically outside of protected areas where predation risks are greatest. A frequency-related spatial analysis of movement-step lengths reveal that rest cycles related to the spatial distribution of critical resources (i.e., forage and water) are responsible for creating the observed patterns. Our approach generates unique information regarding the spatial-temporal interplay between environmental and individual characteristics, providing an original approach for understanding the movement ecology of individual animals and the spatial organization of animal populations.
Movement ecology of migration in turkey vultures
Authors: Mandel J. T. , Bildstein K. L. , Bohrer G. , Winkler D. W.
Published: December 2008

We develop individual-based movement ecology models (MEM) to explore turkey vulture (Cathartes aura) migration decisions at both hourly and daily scales. Vulture movements in 10 migration events were recorded with satellite-reporting GPS sensors, and flight behavior was observed visually, aided by on-the-ground VHF radio-tracking. We used the North American Regional Reanalysis dataset to obtain values for wind speed, turbulent kinetic energy (TKE), and cloud height and used a digital elevation model for a measure of terrain ruggedness. A turkey vulture fitted with a heart-rate logger during 124 h of flight during 38 contiguous days showed only a small increase in mean heart rate as distance traveled per day increased, which suggests that, unlike flapping, soaring flight does not lead to greatly increased metabolic costs. Data from 10 migrations for 724 hourly segments and 152 daily segments showed that vultures depended heavily upon high levels of TKE in the atmospheric boundary layer to increase flight distances and maintain preferred bearings at both hourly and daily scales. We suggest how the MEM can be extended to other spatial and temporal scales of avian migration. Our success in relating model-derived atmospheric variables to migration indicates the potential of using regional reanalysis data, as here, and potentially other regional, higher-resolution, atmospheric models in predicting changing movement patterns of soaring birds under various scenarios of climate and land use change.
Geomagnetic imprinting: A unifying hypothesis of long-distance natal homing in salmon and sea turtles
Authors: Lohmann Kenneth J. , Putman Nathan F. , Lohmann Catherine M. F.
Published: December 2008

Several marine animals, including salmon and sea turtles, disperse across vast expanses of ocean before returning as adults to their natal areas to reproduce. How animals accomplish such feats of natal homing has remained an enduring mystery. Salmon are known to use chemical cues to identify their home rivers at the end of spawning migrations. Such cues, however, do not extend far enough into the ocean to guide migratory movements that begin in open-sea locations hundreds or thousands of kilometers away. Similarly, how sea turtles reach their nesting areas from distant sites is unknown. However, both salmon and sea turtles detect the magnetic field of the Earth and use it as a directional cue. In addition, sea turtles derive positional information from two magnetic elements (inclination angle and intensity) that vary predictably across the globe and endow different geographic areas with unique magnetic signatures. Here we propose that salmon and sea turtles imprint on the magnetic field of their natal areas and later use this information to direct natal homing. This novel hypothesis provides the first plausible explanation for how marine animals can navigate to natal areas from distant oceanic locations. The hypothesis appears to be compatible with present and recent rates of field change (secular variation); one implication, however, is that unusually rapid changes in the Earth's field, as occasionally occur during geomagnetic polarity reversals, may affect ecological processes by disrupting natal homing, resulting in widespread colonization events and changes in population structure.
Fractal reorientation clocks: Linking animal behavior to statistical patterns of search
Authors: Bartumeus Frederic , Levin Simon A.
Published: December 2008

The movement ecology framework depicts animal movement as the result of the combined effects of internal and external constraints on animal navigation and motion capacities. Nevertheless, there are still fundamental problems to understand how these modulations take place and how they might be translated into observed statistical properties of animal trajectories. Of particular interest, here, is the general idea of intermittence in animal movement. Intermittent locomotion assumes that animal movement is, in essence, discrete. The existence of abrupt interruptions in an otherwise continuous flow of movement allows for the possibility of reorientations, that is, to break down previous directional memories of the trajectory. In this study, we explore the potential links between intermittent locomotion, reorientation behavior, and search efficiency. By means of simulations we show that the incorporation of Lévy intermittence in an otherwise nonintermittent search strongly modifies encounter rates. The result is robust to different types of landscapes (i.e., target density and spatial distribution), and spatial dimensions (i.e., 2D, 3D). We propose that Lévy intermittence may come from reorientation mechanisms capable of organizing directional persistence on time (i.e., fractal reorientation clocks), and we rationalize that the explicit distinction between scanning and reorientation mechanisms is essential to make accurate statistical inferences from animal search behavior. Finally, we provide a statistical tool to judge the existence of episodic and strong reorientation behaviors capable of modifying relevant properties of stochastic searches, ultimately controlling the chances of finding unknown located items.
The movement ecology and dynamics of plant communities in fragmented landscapes
Authors: Damschen Ellen I. , Brudvig Lars A. , Haddad Nick M. , Levey Douglas J. , Orrock John L. , Tewksbury Joshua J.
Published: December 2008

A conceptual model of movement ecology has recently been advanced to explain all movement by considering the interaction of four elements: internal state, motion capacity, navigation capacities, and external factors. We modified this framework to generate predictions for species richness dynamics of fragmented plant communities and tested them in experimental landscapes across a 7-year time series. We found that two external factors, dispersal vectors and habitat features, affected species colonization and recolonization in habitat fragments and their effects varied and depended on motion capacity. Bird-dispersed species richness showed connectivity effects that reached an asymptote over time, but no edge effects, whereas wind-dispersed species richness showed steadily accumulating edge and connectivity effects, with no indication of an asymptote. Unassisted species also showed increasing differences caused by connectivity over time, whereas edges had no effect. Our limited use of proxies for movement ecology (e.g., dispersal mode as a proxy for motion capacity) resulted in moderate predictive power for communities and, in some cases, highlighted the importance of a more complete understanding of movement ecology for predicting how landscape conservation actions affect plant community dynamics.
Tracking butterfly movements with harmonic radar reveals an effect of population age on movement distance
Authors: Ovaskainen Otso , Smith Alan D. , Osborne Juliet L. , Reynolds Don R. , Carreck Norman L. , Martin Andrew P. , Niitepõld Kristjan , Hanski Ilkka
Published: December 2008

We used harmonic radar to track freely flying Glanville fritillary butterfly (Melitaea cinxia) females within an area of 30 ha. Butterflies originated from large and continuous populations in China and Estonia, and from newly established or old (> 5 years) small local populations in a highly fragmented landscape in Finland. Caterpillars were raised under common garden conditions and unmated females were tested soon after eclosion. The reconstructed flight paths for 66 individuals comprised a total distance of 51 km with high spatial resolution. Butterflies originating from large continuous populations and from old local populations in Finland exhibited similar movement behaviors, whereas butterflies originating from newly established local populations in the fragmented landscape in Finland moved significantly more than the others. There was no difference in the lengths of individual flight bouts, but the new-population females flew more frequently, resulting in longer daily movement tracks. The flight activity of all individuals was affected by environmental conditions, peaking at 19–23°C (depending on population type), in the early afternoon, and during calm weather. Butterflies from all population types showed a strong tendency to follow habitat edges between the open study area and the neighboring woodlands.
Understanding strategies for seed dispersal by wind under contrasting atmospheric conditions
Authors: Wright S. Joseph , Trakhtenbrot Ana , Bohrer Gil , Detto Matteo , Katul Gabriel G. , Horvitz Nir , Muller-Landau Helene C. , Jones Frank A. , Nathan Ran
Published: December 2008

Traits associated with seed dispersal vary tremendously among sympatric wind-dispersed plants. We used two contrasting tropical tree species, seed traps, micrometeorology, and a mechanistic model to evaluate how variation in four key traits affects seed dispersal by wind. The conceptual framework of movement ecology, wherein external factors (wind) interact with internal factors (plant traits) that enable movement and determine when and where movement occurs, fully captures the variable inputs and outputs of wind dispersal models and informs their interpretation. We used model calculations to evaluate the spatial pattern of dispersed seeds for the 16 factorial combinations of four traits. The study species differed dramatically in traits related to the timing of seed release, and a strong species by season interaction affected most aspects of the spatial pattern of dispersed seeds. A rich interplay among plant traits and seasonal differences in atmospheric conditions caused this interaction. Several of the same plant traits are crucial for both seed dispersal and other aspects of life history variation. Observed traits that limit dispersal are likely to be constrained by their life history consequences.
The chromosome 3p21.3-encoded gene,
LIMD1
, is a critical tumor suppressor involved in human lung cancer development
Authors: Sharp Tyson V. , Al-Attar Ahmad , Foxler Daniel E. , Ding Li , de A. Vallim Thomas Q. , Zhang Yining , Nijmeh Hala S. , Webb Thomas M. , Nicholson Andrew G. , Zhang Qunyuan , Kraja Aldi , Spendlove Ian , Osborne John , Mardis Elaine , Longmore Gregory D.
Published: December 2008

Loss of heterozygosity (LOH) and homozygous deletions at chromosome 3p21.3 are common in both small and nonsmall cell lung cancers, indicating the likely presence of tumor suppressor genes (TSGs). Although genetic and epigenetic changes within this region have been identified, the functional significance of these changes has not been explored. Concurrent protein expression and genetic analyses of human lung tumors coupled with functional studies have not been done. Here, we show that expression of the 3p21.3 gene,
LIMD1
, is frequently down-regulated in human lung tumors. Loss of LIMD1 expression occurs through a combination of gene deletion, LOH, and epigenetic silencing of transcription without evidence for coding region mutations. Experimentally,
LIMD1
is a bona fide TSG.
Limd1
−/−
mice are predisposed to chemical-induced lung adenocarcinoma and genetic inactivation of
Limd1
in mice heterozygous for oncogenic K-Ras
G12D
markedly increased tumor initiation, promotion, and mortality. Thus, we conclude that
LIMD1
is a validated chromosome 3p21.3 tumor-suppressor gene involved in human lung cancer development. LIMD1 is a LIM domain containing adapter protein that localizes to E-cadherin cell–cell adhesive junctions, yet also translocates to the nucleus where it has been shown to function as an RB corepressor. As such, LIMD1 has the potential to communicate cell extrinsic or environmental cues with nuclear responses.
Role of prostaglandin D
2
receptor DP as a suppressor of tumor hyperpermeability and angiogenesis in vivo
Authors: Murata Takahisa , Lin Michelle I. , Aritake Kosuke , Matsumoto Shigeko , Narumiya Shu , Ozaki Hiroshi , Urade Yoshihiro , Hori Masatoshi , Sessa William C.
Published: December 2008

Although COX-dependent production of prostaglandins (PGs) is known to be crucial for tumor angiogenesis and growth, the role of PGD
2
remains virtually unknown. Here we show that PGD
2
receptor (DP) deficiency enhances tumor progression accompanied by abnormal vascular expansion. In tumors, angiogenic endothelial cells highly express DP receptor, and its deficiency accelerates vascular leakage and angiogenesis. Administration of a synthetic DP agonist, BW245C, markedly suppresses tumor growth as well as tumor hyperpermeability in WT mice, but not in DP-deficient mice. In a corneal angiogenesis assay and a modified Miles assay, host DP deficiency potentiates angiogenesis and vascular hyperpermeability under COX-2-active situation, whereas exogenous administration of BW245C strongly inhibits both angiogenic properties in WT mice. In an in vitro assay, BW245C does not affect endothelial migration and tube formation, processes that are necessary for angiogenesis; however, it strongly improves endothelial barrier function via an increase in intracellular cAMP production. Our results identify PGD
2
/DP receptor as a new regulator of tumor vascular permeability, indicating DP agonism may be exploited as a potential therapy for the treatment of cancer.
The photoreversible fluorescent protein iLOV outperforms GFP as a reporter of plant virus infection
Authors: Chapman Sean , Faulkner Christine , Kaiserli Eirini , Garcia-Mata Carlos , Savenkov Eugene I. , Roberts Alison G. , Oparka Karl J. , Christie John M.
Published: December 2008

Fluorescent proteins (FPs) based on green fluorescent protein (GFP) are widely used throughout cell biology to study protein dynamics, and have extensive use as reporters of virus infection and spread. However, FP-tagging of viruses is limited by the constraints of viral genome size resulting in FP loss through recombination events. To overcome this, we have engineered a smaller (≈10 kDa) flavin-based alternative to GFP (≈25 kDa) derived from the light, oxygen or voltage-sensing (LOV) domain of the plant blue light receptor, phototropin. Molecular evolution and Tobacco mosaic virus (TMV)-based expression screening produced LOV variants with improved fluorescence and photostability
in planta.
One variant in particular, designated iLOV, possessed photophysical properties that made it ideally suited as a reporter of subcellular protein localization in both plant and mammalian cells. Moreover, iLOV fluorescence was found to recover spontaneously after photobleaching and displayed an intrinsic photochemistry conferring advantages over GFP-based FPs. When expressed either as a cytosolic protein or as a viral protein fusion, iLOV functioned as a superior reporter to GFP for monitoring local and systemic infections of plant RNA viruses. iLOV, therefore, offers greater utility in FP-tagging of viral gene products and represents a viable alternative where functional protein expression is limited by steric constraints or genome size.
A crystallographic snapshot of tyrosine
trans
-phosphorylation in action
Authors: Chen Huaibin , Xu Chong-Feng , Ma Jinghong , Eliseenkova Anna V. , Li Wanqing , Pollock Pamela M. , Pitteloud Nelly , Miller W. Todd , Neubert Thomas A. , Mohammadi Moosa
Published: December 2008

Tyrosine
trans
-phosphorylation is a key event in receptor tyrosine kinase signaling, yet, the structural basis for this process has eluded definition. Here, we present the crystal structure of the FGF receptor 2 kinases caught in the act of
trans
-phosphorylation of Y769, the major C-terminal phosphorylation site. The structure reveals that enzyme- and substrate-acting kinases engage each other through elaborate and specific interactions not only in the immediate vicinity of Y769 and the enzyme active site, but also in regions that are as much of 18 Å away from D626, the catalytic base in the enzyme active site. These interactions lead to an unprecedented level of specificity and precision during the
trans
-phosphorylation on Y769. Time-resolved mass spectrometry analysis supports the observed mechanism of
trans
-phosphorylation. Our data provide a molecular framework for understanding the mechanism of action of Kallmann syndrome mutations and the order of
trans
-phosphorylation reactions in FGFRs. We propose that the salient mechanistic features of Y769
trans
-phosphorylation are applicable to
trans
-phosphorylation of the equivalent major phosphorylation sites in many other RTKs.
Enhanced translocation of single DNA molecules through α-hemolysin nanopores by manipulation of internal charge
Authors: Maglia Giovanni , Restrepo Marcela Rincon , Mikhailova Ellina , Bayley Hagan
Published: December 2008

Both protein and solid-state nanopores are under intense investigation for the analysis of nucleic acids. A crucial advantage of protein nanopores is that site-directed mutagenesis permits precise tuning of their properties. Here, by augmenting the internal positive charge within the α-hemolysin pore and varying its distribution, we increase the frequency of translocation of a 92-nt single-stranded DNA through the pore at +120 mV by ≈10-fold over the wild-type protein and dramatically lower the voltage threshold at which translocation occurs, e.g., by 50 mV for 1 event·s
−1
·μM
−1
. Further, events in which DNA enters the pore, but is not immediately translocated, are almost eliminated. These experiments provide a basis for improved nucleic acid analysis with protein nanopores, which might be translated to solid-state nanopores by using chemical surface modification.
Rods-cones and melanopsin detect light and dark to modulate sleep independent of image formation
Authors: Altimus C. M. , Güler A. D. , Villa K. L. , McNeill D. S. , LeGates T. A. , Hattar S.
Published: December 2008

Light detected in the retina modulates several physiological processes including circadian photo-entrainment and pupillary light reflex. Intrinsically photosensitive retinal ganglion cells (ipRGCs) convey rod-cone and melanopsin-driven light input to the brain. Using EEGs and electromyograms, we show that acute light induces sleep in mice during their nocturnal active phase whereas acute dark awakens mice during their diurnal sleep phase. We used retinal mutant mouse lines that lack (
i
) the ipRGCs, (
ii
) the photo-transduction pathways of rods and cones, or (
iii
) the melanopsin protein and showed that the influence of light and dark on sleep requires both rod-cone and melanopsin signaling through ipRGCs and is independent of image formation. We further show that, although acute light pulses overcome circadian and homeostatic drives for sleep, upon repeated light exposures using a 3.5 h/3.5 h light/dark cycle, the circadian and homeostatic drives override the light input. Thus, in addition to their known role in aligning circadian physiology with day and night, ipRGCs also relay light and dark information from both rod-cone and melanopsin-based pathways to modulate sleep and wakefulness.
Anopheles gambiaemales produce and transfer the vitellogenic steroid hormone 20-hydroxyecdysone to females during mating
Authors: Pondeville Emilie , Maria Annick , Jacques Jean-Claude , Bourgouin Catherine , Dauphin-Villemant Chantal
Published: December 2008

In female insects, the steroid hormone 20-hydroxyecdysone (20E) plays a major role in activating vitellogenesis, a process required for egg development. By contrast with vertebrates, production of large amounts of hormonal steroids has not been reported in adult male insects. In the present study, we analyzed steroidogenesis in both male and female adult of the malaria mosquitoAnopheles gambiaeand we found thatA. gambiaemale mosquitoes produce high amounts of the steroid hormone 20E. Importantly, we found that male accessory glands, but not testes, are the source of 20E. Moreover, this steroid hormone is stored in male accessory glands and delivered to females during mating. These findings suggest that male 20E may not act as a true male sex steroid, but more likely as an allohormone. Our results give new insights into species-specific physiological processes that govern the reproductive success of the malaria mosquito. This could thus lead to the identification of new target genes for manipulating male and/or female reproductive success, a promising way to reduce or eliminate mosquito population and therefore to control malaria transmission.
Genome-wide analysis reveals Sall4 to be a major regulator of pluripotency in murine-embryonic stem cells
Authors: Yang Jianchang , Chai Li , Fowles Taylor C. , Alipio Zaida , Xu Dan , Fink Louis M. , Ward David C. , Ma Yupo
Published: December 2008

Embryonic stem cells have potential utility in regenerative medicine because of their pluripotent characteristics. Sall4, a zinc-finger transcription factor, is expressed very early in embryonic development with Oct4 and Nanog, two well-characterized pluripotency regulators. Sall4 plays an important role in governing the fate of stem cells through transcriptional regulation of both Oct4 and Nanog. By using chromatin immunoprecipitation coupled to microarray hybridization (ChIP-on-chip), we have mapped global gene targets of Sall4 to further investigate regulatory processes in W4 mouse ES cells. A total of 3,223 genes were identified that were bound by the Sall4 protein on duplicate assays with high confidence, and many of these have major functions in developmental and regulatory pathways. Sall4 bound approximately twice as many annotated genes within promoter regions as Nanog and approximately four times as many as Oct4. Immunoprecipitation revealed a heteromeric protein complex(es) between Sall4, Oct4, and Nanog, consistent with binding site co-occupancies. Decreasing Sall4 expression in W4 ES cells decreases the expression levels of Oct4, Sox2, c-Myc, and Klf4, four proteins capable of reprogramming somatic cells to an induced pluripotent state. Further, Sall4 bound many genes that are regulated in part by chromatin-based epigenetic events mediated by polycomb-repressive complexes and bivalent domains. This suggests that Sall4 plays a diverse role in regulating stem cell pluripotency during early embryonic development through integration of transcriptional and epigenetic controls.
Light-arousal and circadian photoreception circuits intersect at the large PDF cells of the
Drosophila
brain
Authors: Shang Yuhua , Griffith Leslie C. , Rosbash Michael
Published: December 2008

The neural circuits that regulate sleep and arousal as well as their integration with circadian circuits remain unclear, especially in
Drosophila
. This issue intersects with that of photoreception, because light is both an arousal signal in diurnal animals and an entraining signal for the circadian clock. To identify neurons and circuits relevant to light-mediated arousal as well as circadian phase-shifting, we developed genetic techniques that link behavior to single cell-type resolution within the
Drosophila
central brain. We focused on the unknown function of the 10 PDF-containing large ventral lateral neurons (l-LNvs) of the
Drosophila
circadian brain network and show here that these cells function in light-dependent arousal. They also are important for phase shifting in the late-night (dawn), indicating that the circadian photoresponse is a network property and therefore non-cell-autonomous. The data further indicate that the circuits underlying light-induced arousal and circadian photoentrainment intersect at the l-LNvs and then segregate.
Rapid evolution of Cse4p-rich centromeric DNA sequences in closely related pathogenic yeasts,
Candida albicans
and
Candida dubliniensis
Authors: Padmanabhan Sreedevi , Thakur Jitendra , Siddharthan Rahul , Sanyal Kaustuv
Published: December 2008

The Cse4p-containing centromere regions of
Candida albicans
have unique and different DNA sequences on each of the eight chromosomes. In a closely related yeast,
C. dubliniensis
, we have identified the centromeric histone, CdCse4p, and shown that it is localized at the kinetochore. We have identified putative centromeric regions, orthologous to the
C. albicans
centromeres, in each of the eight
C. dubliniensis
chromosomes by bioinformatic analysis. Chromatin immunoprecipitation followed by PCR using a specific set of primers confirmed that these regions bind CdCse4p
in vivo
. As in
C. albicans
, the CdCse4p-associated core centromeric regions are 3–5 kb in length and show no sequence similarity to one another. Comparative sequence analysis suggests that the Cse4p-rich centromere DNA sequences in these two species have diverged faster than other orthologous intergenic regions and even faster than our best estimated “neutral” mutation rate. However, the location of the centromere and the relative position of Cse4p-rich centromeric chromatin in the orthologous regions with respect to adjacent ORFs are conserved in both species, suggesting that centromere identity is not solely determined by DNA sequence. Unlike known point and regional centromeres of other organisms, centromeres in
C. albicans
and
C. dubliniensis
have no common centromere-specific sequence motifs or repeats except some of the chromosome-specific pericentric repeats that are found to be similar in these two species. We propose that centromeres of these two
Candida
species are of an intermediate type between point and regional centromeres.
HIV infection-associated immune activation occurs by two distinct pathways that differentially affect CD4 and CD8 T cells
Authors: Catalfamo Marta , Di Mascio Michele , Hu Zonghui , Srinivasula Sharat , Thaker Vishakha , Adelsberger Joseph , Rupert Adam , Baseler Michael , Tagaya Yutaka , Roby Gregg , Rehm Catherine , Follmann Dean , Lane H. Clifford
Published: December 2008

HIV infection is characterized by a brisk immune activation that plays an important role in the CD4 depletion and immune dysfunction of patients with AIDS. The mechanism underlying this activation is poorly understood. In the current study, we tested the hypothesis that this activation is the net product of two distinct pathways: the inflammatory response to HIV infection and the homeostatic response to CD4 T cell depletion. Usingex vivoBrdU incorporation of PBMCs from 284 patients with different stages of HIV infection, we found that CD4 proliferation was better predicted by the combination of CD4 depletion and HIV viral load (R2= 0.375,P< 0.001) than by either parameter alone (CD4 T cell counts,R2= 0.202,P< 0.001; HIV viremia,R2= 0.302,P< 0.001). Interestingly, CD8 T cell proliferation could be predicted by HIV RNA levels alone (R2= 0.334,P< 0.001) and this predictive value increased only slightly (R2= 0.346,P< 0.001) when CD4 T cell depletion was taken into account. Consistent with the hypothesis that CD4 T cell proliferation is driven by IL-7 as a homeostatic response to CD4 T cell depletion, levels of phosphorylated STAT-5 were found to be elevated in naive subsets of CD4 and CD8 T cells from patients with HIV infection and in the central memory subset of CD4 T cells. Taken together these data demonstrate that at least two different pathways lead to immune activation of T cells in patients with HIV infection and these pathways differentially influence CD4 and CD8 T cell subsets.
Bivalent domains enforce transcriptional memory of DNA methylated genes in cancer cells
Authors: Rodriguez Jairo , Muñoz Mar , Vives Laura , Frangou Costas G. , Groudine Mark , Peinado Miguel A.
Published: December 2008

Silencing of multiple cancer-related genes is associated with de novo methylation of linked CpG islands. Additionally, bivalent histone modification profiles characterized by the juxtaposition of active and inactive histone marks have been observed in genes that become hypermethylated in cancer. It is unknown how these ambiguous epigenetic states are maintained and how they interrelate with adjacent genomic regions with different epigenetic landscapes. Here, we present the analysis of a set of neighboring genes, including many frequently silenced in colon cancer cells, in a chromosomal region at 5q35.2 spanning 1.25 Mb. Promoter DNA methylation occurs only at genes maintained at a low transcriptional state and is characterized by the presence of bivalent histone marks, namely trimethylation of lysines 4 and 27 in histone 3. Chemically induced hyperacetylation and DNA demethylation lead to up-regulation of silenced genes in this locus yet do not resolve bivalent domains into a domain-wide active chromatin conformation. In contrast, active genes in the region become down-regulated after drug treatment, accompanied by a partial loss of chromatin domain boundaries and spreading of the inactive histone mark trimethylated lysine 27 in histone 3. Our results demonstrate that bivalent domains mark the promoters of genes that will become DNA methylated in adult tumor cells to enforce transcriptional silence. These bivalent domains not only remain upon drug induced gene reactivation, but also spread over adjacent CpG islands. These results may have important implications in understanding and managing epigenetic therapies of cancer.
Noninvasive prenatal diagnosis of monogenic diseases by digital size selection and relative mutation dosage on DNA in maternal plasma
Authors: Lun Fiona M. F. , Tsui Nancy B. Y. , Chan K. C. Allen , Leung Tak Y. , Lau Tze K. , Charoenkwan Pimlak , Chow Katherine C. K. , Lo Wyatt Y. W. , Wanapirak Chanane , Sanguansermsri Torpong , Cantor Charles R. , Chiu Rossa W. K. , Lo Y. M. Dennis
Published: December 2008

Prenatal diagnosis of monogenic diseases, such as cystic fibrosis and β-thalassemia, is currently offered as part of public health programs. However, current methods based on chorionic villus sampling and amniocentesis for obtaining fetal genetic material pose a risk to the fetus. Since the discovery of cell-free fetal DNA in maternal plasma, the noninvasive prenatal assessment of paternally inherited traits or mutations has been achieved. Due to the presence of background maternal DNA, which interferes with the analysis of fetal DNA in maternal plasma, noninvasive prenatal diagnosis of maternally inherited mutations has not been possible. Here we describe a digital relative mutation dosage (RMD) approach that determines if the dosages of the mutant and wild-type alleles of a disease-causing gene are balanced or unbalanced in maternal plasma. When applied to the testing of women heterozygous for the CD41/42 (–CTTT) and hemoglobin E mutations on
HBB
, digital RMD allows the fetal genotype to be deduced. The diagnostic performance of digital RMD is dependent on interplay between the fractional fetal DNA concentration and number of DNA molecules in maternal plasma. To achieve fetal genotype diagnosis at lower volumes of maternal plasma, fetal DNA enrichment is desired. We thus developed a digital nucleic acid size selection (NASS) strategy that effectively enriches the fetal DNA without additional plasma sampling or experimental time. We show that digital NASS can work in concert with digital RMD to increase the proportion of cases with classifiable fetal genotypes and to bring noninvasive prenatal diagnosis of monogenic diseases closer to reality.
Efficient transposition of the
Tol2
transposable element from a single-copy donor in zebrafish
Authors: Urasaki Akihiro , Asakawa Kazuhide , Kawakami Koichi
Published: December 2008

The
Tol2
transposable element is a powerful genetic tool in model vertebrates and has been used for transgenesis, insertional mutagenesis, gene trapping, and enhancer trapping. However, an
in vivo
transposition system using
Tol2
has not yet been developed. Here we report the
in vivo Tol2
transposition system in a model vertebrate, zebrafish. First, we constructed transgenic zebrafish that carried single-copy integrations of
Tol2
on the genome and injected transposase mRNA into one-cell stage embryos. The
Tol2
insertions were mobilized efficiently in the germ lineage. We then mobilized an insertion of the
Tol2
gene trap construct in the
nup214
gene, which caused a recessive lethal mutant phenotype, and demonstrated that this method is applicable to the isolation of revertants from a transposon insertional mutant. Second, we constructed transgenic fish carrying the transposase cDNA under the control of the
hsp70
promoter. Double-transgenic fish containing the transposase gene and a single-copy
Tol2
insertion were treated with heat shock at the adult stage. We found that transposition can be induced efficiently in the male germ cells. We analyzed new integration sites and found that the majority (83%) of them were mapped on chromosomes other than the transposon donor chromosomes and that 9% of local hopping events mapped less than 300 kb away from the donor loci. Our present study demonstrates that the
in vivo Tol2
transposition system is useful for creating genome-wide insertions from a single-copy donor and should facilitate functional genomics and transposon biology in vertebrates.
NKT cells prevent chronic joint inflammation after infection withBorrelia burgdorferi
Authors: Tupin Emmanuel , Benhnia Mohammed Rafii-El-Idrissi , Kinjo Yuki , Patsey Rebeca , Lena Christopher J. , Haller Matthew C. , Caimano Melissa J. , Imamura Masakazu , Wong Chi-Huey , Crotty Shane , Radolf Justin D. , Sellati Timothy J. , Kronenberg Mitchell
Published: December 2008

Borrelia burgdorferiis the etiologic agent of Lyme disease, a multisystem inflammatory disorder that principally targets the skin, joints, heart, and nervous system. The role of T lymphocytes in the development of chronic inflammation resulting fromB. burgdorferiinfection has been controversial. We previously showed that natural killer T (NKT) cells with an invariant (i) TCR α chain (iNKT cells) recognize glycolipids fromB. burgdorferi, but did not establish an in vivo role foriNKT cells in Lyme disease pathogenesis. Here, we evaluate the importance ofiNKT cells for host defense against these pathogenic spirochetes by using Vα14iNKT cell-deficient (Jα18−/−) BALB/c mice. On tick inoculation withB. burgdorferi,Jα18−/−mice exhibited more severe and prolonged arthritis as well as a reduced ability to clear spirochetes from infected tissues. Vα14iNKT cell deficiency also resulted in increased production of antibodies directed against bothB. burgdorferiprotein antigens and borrelial diacylglycerols; the latter finding demonstrates that anti-glycolipid antibody production does not require cognate help from Vα14iNKT cells. Vα14iNKT cells in infected wild-type mice expressed surface activation markers and produced IFNγ in vivo after infection, suggesting a participatory role for this unique population in cellular immunity. Our data are consistent with the hypothesis that the antigen-specific activation of Vα14iNKT cells is important for the prevention of persistent joint inflammation and spirochete clearance, and they counter the long-standing notion that humoral rather than cellular immunity is sufficient to facilitate Lyme disease resolution.
Contribution of KCNQ2 and KCNQ3 to the medium and slow afterhyperpolarization currents
Authors: Tzingounis Anastassios V. , Nicoll Roger A.
Published: December 2008

Benign familial neonatal convulsion (BNFC) is a neurological disorder caused by mutations in the potassium channel genes KCNQ2 and KCNQ3, which are thought to contribute to the medium afterhyperpolarization (mAHP). Despite their importance in normal brain function, it is unknown whether they invariably function as heteromeric complexes. Here, we examined the contribution of KCNQ3 and KCNQ2 in mediating the apamin-insensitive mAHP current (ImAHP) in hippocampus. The ImAHP was not impaired in CA1 pyramidal neurons from mice genetically deficient for either KCNQ3 or KCNQ2 but was reduced ≈50% in dentate granule cells. While recording from KCNQ-deficient mice, we observed that the calcium-activated slow afterhyperpolarization current (IsAHP) was also reduced in dentate granule cells, suggesting that KCNQ channels might also contribute to this potassium current whose molecular identity is unknown. Further pharmacological and molecular experiments manipulating KCNQ channels provided evidence in support of this possibility. Together our data suggest that multiple KCNQ subunit compositions can mediate the ImAHP, and that the very same subunits may also contribute to the IsAHP. We also present data suggesting that the neuronal calcium sensor protein hippocalcin may allow for these dual signaling processes.
A dimer-specific function of the transcription factor NFATp
Authors: Falvo James V. , Lin Charles H. , Tsytsykova Alla V. , Hwang Peter K. , Thanos Dimitris , Goldfeld Anne E. , Maniatis Tom
Published: December 2008

The transcription factor NFATp integrates multiple signal transduction pathways through coordinate binding with basic-region leucine zipper (bZIP) proteins and other transcription factors. The NFATp monomer, even in the absence of its activation domains, recruits bZIP proteins to canonical NFAT–bZIP composite DNA elements. By contrast, the NFATp dimer and its bZIP partner bind noncooperatively to the NFAT–bZIP element of the tumor necrosis factor (
TNF
) gene promoter. This observation raises the possibility that the function of the activation domains of NFATp is dimer-specific. Here, we determine the consensus DNA binding site of the NFATp dimer, describe monomer- and dimer-specific NFATp–DNA contact patterns, and demonstrate that NFATp dimerization and dimer-specific activation subdomains are required for transcriptional activation from the
TNF
NFAT–bZIP element. We also show that these NFATp subdomains interact with the coactivator CBP (CREB-binding protein), which is required for NFATp-dependent
TNF
gene transcription. Thus, the context-specific function of the activation domains of NFAT can be potentiated by DNA-directed dimerization.
Overlapping functions of the four class XI myosins in Arabidopsis growth, root hair elongation, and organelle motility
Authors: Prokhnevsky Alexey I. , Peremyslov Valera V. , Dolja Valerian V.
Published: December 2008

Flowering plants have evolved multigene families of the class XI myosin motors, the functions of which remain poorly understood. Here, we investigated functional profiles of the Arabidopsis myosins that belong to two paralogous pairs, XI-K/XI-1 and XI-2/XI-B, using single and double gene-knockout mutants. It was found that the myosins XI-K, XI-2, and XI-B, but not XI-1 have overlapping and additive roles in the root hair elongation. A nonidentical set of the three myosins, XI-K, XI-1, and XI-2, exhibited partially redundant and additive roles in the transport of Golgi stacks, peroxisomes, and mitochondria. Conspicuously, the double
xi-k/1
knockout plants that showed the largest cumulative reduction of the organelle velocities also exhibited a stunted plant growth and reduced fecundity phenotype. Collectively, these results suggest that the rapid, myosin-powered organelle trafficking is required for the optimal plant growth, whereas a distinct myosin function, presumably the vesicular transport, is involved in elongation of the root hairs. In addition, our data imply that the myosin gene duplication in plants has been followed by a gradual functional specialization of the resulting pairs of myosin paralogs.
Radial stretch reveals distinct populations of mechanosensitive mammalian somatosensory neurons
Authors: Bhattacharya Martha R. C. , Bautista Diana M. , Wu Karin , Haeberle Henry , Lumpkin Ellen A. , Julius David
Published: December 2008

Primary afferent somatosensory neurons mediate our sense of touch in response to changes in ambient pressure. Molecules that detect and transduce thermal stimuli have been recently identified, but mechanisms underlying mechanosensation, particularly in vertebrate organisms, remain enigmatic. Traditionally, mechanically evoked responses in somatosensory neurons have been assessed one cell at a time by recording membrane currents in response to application of focal pressure, suction, or osmotic challenge. Here, we used radial stretch in combination with live-cell calcium imaging to gain a broad overview of mechanosensitive neuronal subpopulations. We found that different stretch intensities activate distinct subsets of sensory neurons as defined by size, molecular markers, or pharmacological attributes. In all subsets, stretch-evoked responses required extracellular calcium, indicating that mechanical force triggers calcium influx. This approach extends the repertoire of stimulus paradigms that can be used to examine mechanotransduction in mammalian sensory neurons, facilitating future physiological and pharmacological studies.
In vitro assembly of the
Tomato bushy stunt virus
replicase requires the host Heat shock protein 70
Authors: Pogany Judit , Stork Jozsef , Li Zhenghe , Nagy Peter D.
Published: December 2008

To gain insights into the functions of a viral RNA replicase, we have assembled in vitro and entirely from nonplant sources, a fully functional replicase complex of
Tomato bushy stunt virus
(TBSV). The formation of the TBSV replicase required two purified recombinant TBSV replication proteins, which were obtained from
E. coli
, the viral RNA replicon, rATP, rGTP, and a yeast cell-free extract. The in vitro assembly of the replicase took place in the membraneous fraction of the yeast extract, in which the viral replicase-RNA complex became RNase- and proteinase-resistant. The assembly of the replicase complex required the heat shock protein 70 (Hsp70 = yeast Ssa1/2p) present in the soluble fraction of the yeast cell-free extract. The assembled TBSV replicase performed a complete replication cycle, synthesizing RNA complementary to the provided RNA replicon and using the complementary RNA as template to synthesize new TBSV replicon RNA.
Smoking and psychological health in relation to country of origin
Authors: Lyvers Michael , Hall Tessa , Bahr Mark
Published: December 2008

In English‐speaking, Western‐Anglo countries, where smoking has become stigmatized in recent decades as a result of widespread anti‐smoking campaigns, smokers commonly report poorer psychological health on average than nonsmokers do. This may be indirectly related to the strong pressures to quit in such countries, as poorer psychological health is associated with a reduced likelihood of quitting, thus leading to a selection bias for smokers with relatively poorer psychological health. In the present study, 147 smoker and nonsmoker participants either came from Western‐Anglo countries where smoking has become stigmatized (Australia, Canada, USA) or countries in regions where smoking remains relatively more accepted (Asia, Latin America, Europe). Smokers and nonsmokers were assessed on a widely used self‐report measure of anxiety, depression, and stress. Multivariate analysis revealed a significant interaction between smoker status (smoker, nonsmoker) and country of origin (Western‐Anglo, other) on psychological health ratings, with univariate analysis showing a significant interaction on anxiety scores. Among those from Western‐Anglo countries, smokers reported significantly higher levels of anxiety than nonsmokers did, whereas there was no difference in anxiety between smokers and nonsmokers from other countries. There was no difference in the number of cigarettes smoked per day between the samples of smokers, indicating very similar levels of nicotine intake in the two groups. The findings support the notion that a selection bias for smokers with relatively poorer psychological health is occurring in Western‐Anglo countries.
A comparative study between FEA, trepanning and neutron strain diffraction on residual stresses in flash-butt welded rails
Authors: Tawfik D. , Mutton P.J. , Kirstein O. , Chiu W.K.
Published: December 2008

This paper compares three independent methods for deriving the residual stresses distribution in AS60 normal cooled flash-butt welded rail. A numerical technique utilised a sequentially coupled thermo-mechanical analysis with representative temperature dependent and phase transformation properties of the rail steel. The numerical model also incorporated an element removal regime to assess the effect of stress relaxation when slicing a plate section from a welded rail section for neutron stress mapping. Two experimental techniques were used to quantify the magnitude of residual stresses in the weld; these were strain gauging and trepanning, and neutron diffraction (ND). The results showed satisfactory correlation between the residual stress distribution obtained from the numerical analysis and the strain gauge/trepanning data and ND stress mapping,respectively. The ND and numerical analysis both confirmed that the tensile residual stresses in both vertical and longitudinal directions are concentrated in the web region, despite a significant relaxation as a result of the sectioning method used to obtain the plate section for neutron stress mapping.
Prison health advocacy and its changing boundaries
Authors: Awofeso Niyi
Published: December 2008

Advocacy is an important tool for translating population health objectives and research findings into policy and practice, as well as for enhancing stakeholder support for programmes and activities with a potential to improve the health of populations. At the inception of modern prisons, health advocacy approaches focused on appealing to humanitarian and religious sentiments of stakeholders to improve the well‐being of prisoners. This approach achieved limited results, not least because of persistent apathy of custodial authorities and the public to prisoners’ wellbeing. From the mid twentieth century onwards, a constitutional and human rights approach evolved, with courts becoming actively involved
in mandating minimum health standards in prisons. Penal populism eroded public support for a judicial recourse to improving prison health services, and encouraged governments to institute
procedural barriers to prisoner‐initiated litigation. The author proposes an approach premised on public health principles as an appropriate platform to advocate for improvements in prison health services in this era. Such an advocacy platform combines the altruistic goals of the humanitarian and constitutional rights approaches with an appeal to community’s self‐interest by alerting the public to the social, financial and health implications inherent in released prisoners suffering from major communicable and chronic diseases re‐entering the community.