bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic subtraction profiling identifies genes essential for Arabidopsisreproduction and reveals interaction between the female gametophyte and the maternal sporophyte
Authors: Johnston Amal J , Meier Patrick , Gheyselinck Jacqueline , Wuest Samuel EJ , Federer Michael , Schlagenhauf Edith , Becker Jörg D , Grossniklaus Ueli 
Published: October 2007

Abstract
Background
The embryo sac contains the haploid maternal cell types necessary for double fertilization and subsequent seed development in plants. Large-scale identification of genes expressed in the embryo sac remains cumbersome because of its inherent microscopic and inaccessible nature. We used genetic subtraction and comparative profiling by microarray between the Arabidopsis thaliana wild-type and a sporophytic mutant lacking an embryo sac in order to identify embryo sac expressed genes in this model organism. The influences of the embryo sac on the surrounding sporophytic tissues were previously thought to be negligible or nonexistent; we investigated the extent of these interactions by transcriptome analysis.

Results
We identified 1,260 genes as embryo sac expressed by analyzing both our dataset and a recently reported dataset, obtained by a similar approach, using three statistical procedures. Spatial expression of nine genes (for instance a central cell expressed trithorax-like gene, an egg cell expressed gene encoding a kinase, and a synergid expressed gene encoding a permease) validated our approach. We analyzed mutants in five of the newly identified genes that exhibited developmental anomalies during reproductive development. A total of 527 genes were identified for their expression in ovules of mutants lacking an embryo sac, at levels that were twofold higher than in the wild type.

Conclusion
Identification of embryo sac expressed genes establishes a basis for the functional dissection of embryo sac development and function. Sporophytic gain of expression in mutants lacking an embryo sac suggests that a substantial portion of the sporophytic transcriptome involved in carpel and ovule development is, unexpectedly, under the indirect influence of the embryo sac.
Expression of human NDRG2 by myeloid dendritic cells inhibits down-regulation of activated leukocyte cell adhesion molecule (ALCAM) and contributes to maintenance of T cell stimulatory activity
Authors: Choi Seung-Chul , Kim Kwang Dong , Kim Jong-Tae , Kim Jae Wha , Lee Hee Gu , Kim Jin-Man , Jang Yong-Suk , Yoon Do-Young , Kim Keun Il , Yang Young , Cho Dae Ho , Lim Jong-Seok 
Published: October 2007

AbstractWe reported previously that N-myc downstream-regulated gene 2 (NDRG2), a member of a new family of differentiation-related genes, is expressed specifically in dendritic cells (DC) differentiated from monocytes, CD34+ progenitor cells, and the myelomonocytic leukemic cell line. In this study, we demonstrate that NDRG2 protein expression is detected, not only in in vitro-differentiated DC but also in primary DC from lymph nodes, thymus, and skin when anti-NDRG2 antibodies are used. As predicted from previous studies investigating the mRNA expression pattern of several types of cell lines, progenitor cells, and DC, NDRG2 protein was expressed strongly in DC. Its expression was detected at significant levels after differentiation from progenitor cells. RNA interference of NDRG2 demonstrated that activated leukocyte cell adhesion molecule (ALCAM) expression is down-regulated specifically in DC differentiated from NDRG2 small interfering RNA (siRNA)-transfected monocytes. This was consistent with our observation that U937 cells transfected with NDRG2 became resistant to the GM-CSF/IL-4-induced ALCAM reduction. Furthermore, DC, which had differentiated from NDRG2 siRNA-transfected monocytes, showed a reduced ability to induce T cell proliferation. Taken together, our results indicate that NDRG2 is able to preserve ALCAM expression during DC differentiation from monocytes under cytokine culture conditions and that its expression helps DC maintain costimulatory signals necessary for T cell stimulation.
Lack of Mutations in the Thyroid Hormone Receptor (TR) α and β Genes but Frequent Hypermethylation of the TRβ Gene in Differentiated Thyroid Tumors
Authors: Joseph Biju , Ji Meiju , Liu Dingxie , Hou Peng , Xing Mingzhao 
Published: October 2007

Abstract
Context: It remains inconclusive whether mutations in thyroid hormone receptor (TR) genes naturally occur in thyroid cancer and whether these genes could be suppressors of this cancer.
Objectives: Our objectives were to examine further mutations of TRα and TRβ genes in thyroid cancer and also to examine their methylation as an epigenetic silencing mechanism in thyroid cancer.
Experimental Design: Instead of using a cDNA sequencing approach used in previous studies, we used genomic DNA to sequence directly the coding regions of the TRα and TRβ genes to search mutations in various differentiated thyroid tumors and used methylation-specific PCR to analyze promoter methylation of these genes. Allelic zygosity status at TRβ was also analyzed.
Results: We found no TRα gene mutation in 17 papillary thyroid cancers (PTCs) and 11 follicular thyroid cancers (FTCs), and no TRβ gene mutation in 16 PTCs and 12 FTCs. We also found no methylation of the TRα gene in 33 PTCs, 31 FTCs, 20 follicular thyroid adenomas (FTAs), and 10 thyroid tumor cell lines. In contrast, we found hypermethylation of the TRβ gene in 10 of 29 (34%) PTCs, 22 of 27 (81%) FTCs, five of 20 (25%) follicular thyroid adenomas, and three of 10 (30%) thyroid tumor cell lines, with the highest prevalence in FTC. We additionally examined loss of heterozygosity at TRβ and found it in three of nine (33%) PTCs and three of nine (33%) FTCs.
Conclusions: Mutation is not common in TR genes, whereas hypermethylation of the TRβ gene as an alternative gene silencing mechanism is highly prevalent in thyroid cancer, particularly FTC, consistent with a possible tumor suppressor role of this gene for FTC.
The long and winding road: influences of intracellular metabolite diffusion on cellular organization and metabolism in skeletal muscle
Authors: Kinsey Stephen T. , Hardy Kristin M. , Locke Bruce R. 
Published: October 2007

SUMMARY
A fundamental principle of physiology is that cells are small in order to minimize diffusion distances for O2 and intracellular metabolites. In skeletal muscle, it has long been recognized that aerobic fibers that are used for steady state locomotion tend to be smaller than anaerobic fibers that are used for burst movements. This tendency reflects the interaction between diffusion distances and aerobic ATP turnover rates, since maximal intracellular diffusion distances are ultimately limited by fiber size. The effect of diffusion distance on O2 flux in muscle has been the subject of quantitative analyses for a century, but the influence of ATP diffusion from mitochondria to cellular ATPases on aerobic metabolism has received much less attention. The application of reaction–diffusion mathematical models to experimental measurements of aerobic metabolic processes has revealed that the extreme diffusion distances between mitochondria found in some muscle fibers do not necessarily limit the rates of aerobic processes per se, as long as the metabolic process is sufficiently slow. However, skeletal muscle fibers from a variety of animals appear to have intracellular diffusion distances and/or fiber sizes that put them on the brink of diffusion limitation. Thus, intracellular metabolite diffusion likely influences the evolution of muscle design and places limits on muscle function.
Reappraisal of the comparative cost of human locomotion using gait-specific allometric analyses
Authors: Rubenson Jonas , Heliams Denham B. , Maloney Shane K. , Withers Philip C. , Lloyd David G. , Fournier Paul A. 
Published: October 2007

SUMMARYThe alleged high net energy cost of running and low net energy cost of walking in humans have played an important role in the interpretation of the evolution of human bipedalism and the biomechanical determinants of the metabolic cost of locomotion. This study re-explores how the net metabolic energy cost of running and walking (J kg–1m–1) in humans compares to that of animals of similar mass using new allometric analyses of previously published data. Firstly, this study shows that the use of the slope of the regression between the rate of energy expenditure and speed to calculate the net energy cost of locomotion overestimates the net cost of human running. Also, the net energy cost of human running is only 17% higher than that predicted based on their mass. This value is not exceptional given that over a quarter of the previously examined mammals and birds have a net energy cost of running that is 17% or more above their allometrically predicted value. Using a new allometric equation for the net energy cost of walking, this study also shows that human walking is 20%less expensive than predicted for their mass. Of the animals used to generate this equation, 25% have a relatively lower net cost of walking compared with their allometrically predicted value. This new walking allometric analysis also indicates that the scaling of the net energy cost of locomotion with body mass is gait dependent. In conclusion, the net costs of running and walking in humans are moderately different from those predicted from allometry and are not remarkable for an animal of its size.
Phonotactic walking paths of field crickets in closed-loop conditions and their simulation using a stochastic model
Authors: Mhatre Natasha , Balakrishnan Rohini 
Published: October 2007

SUMMARYField cricket females localize one of many singing males in the field in closed-loop multi-source conditions. To understand this behaviour, field cricket phonotaxis was investigated in a closed-loop walking phonotaxis paradigm, in response to two simultaneously active speakers playing aphasic calling songs. Female phonotactic paths were oriented towards the louder sound sources, but showed great inter-individual variability. Decisions made in the initial phases were correlated with the overall directions of the paths. Interestingly, the sound pressure levels of stimuli did not greatly influence several features of phonotactic paths such as sinuosity, walking bout lengths and durations. In order to ascertain the extent of our understanding of walking phonotaxis, a stochastic model was used to simulate the behaviour observed in the experiment. The model incorporated data from the experiment and our current understanding of field cricket auditory physiology. This model, based on stochastic turning towards the louder side, successfully recaptured several qualitative and quantitative features of the observed phonotactic paths. The simulation also reproduced the paths observed in a separate outdoor field experiment. Virtual crickets that were unilaterally deafened or had poor ear directionality exhibited walking paths similar to those observed in previous experiments.
Environmental stress affects the expression of a carotenoid-based sexual trait in male zebra finches
Authors: Eraud Cyril , Devevey Godefroy , Gaillard Maria , Prost Josiane , Sorci Gabriele , Faivre Bruno 
Published: October 2007

SUMMARYAbiotic factors including thermal stress are suggested to exert constrains on sexual ornaments through trade-offs between sexual displays and physiological functions related to self-maintenance. Given the health properties of carotenoid pigments, carotenoid-based ornaments offer a relevant context in which to investigate the effect of environmental stress, such as ambient temperature, on the production and maintenance of secondary sexual traits and, also, to explore the proximate mechanisms shaping their expression. In this study, we exposed male zebra finches (Taeniopygia guttata) to environmental stress by exposing them to two temperature regimes (6 and 26°C) over a 4 week period. Simultaneously, half of the males in each temperature group were supplemented with carotenoids, whereas the other half were not. The expression of a carotenoid-based sexual trait(bill colour) and the amount of circulating carotenoids were assessed before and at the end of the experiment. Carotenoid-supplemented males developed a redder bill, but the effect of supplementation was reduced under cold exposure. However, we found evidence that birds facing a cold stress were carotenoid limited, since supplemented males developed redder bills than the non-supplemented ones. Interestingly, while cold-exposed and non-supplemented males developed duller bills, they circulated a higher amount of carotenoids at the end of the experiment compared to the pre-experimental values. Together, these results suggest that ambient temperature might contribute to the modulation of the expression of carotenoid-based ornaments. Our findings suggest that carotenoids are a limiting resource under cold exposure and that they might be prioritized for self-maintenance at the expense of the ornament. The physiological functions related to self-maintenance that might have benefited from carotenoid saving are discussed.
Natural variation in food acquisition mediatedviaaDrosophilacGMP-dependent protein kinase
Authors: Kaun Karla R. , Riedl Craig A. L. , Chakaborty-Chatterjee Munmun , Belay Amsale T. , Douglas Scott J. , Gibbs Allen G. , Sokolowski Marla B. 
Published: October 2007

SUMMARYIn natural environments where food abundance and quality can change drastically over time, animals must continuously alter their food acquisition strategies. Although genetic variation contributes to this plasticity, the specific genes involved and their interactions with the environment are poorly understood. Here we report that natural variation in the Drosophilagene, foraging (for), which encodes a cGMP-dependent protein kinase (PKG), affects larval food acquisition in an environmentally dependent fashion. When food is plentiful, the wild-type rover(forR) allele confers lower food intake and higher glucose absorption than both the wild-type sitter (fors) allele and the mutant fors2 allele. When food is scarce, forR, fors and fors2 larvae increase food intake to a common maximal level, but forRlarvae retain their increased absorption efficiency. Changes in forexpression can induce corrective behavioral modifications in response to food deprivation. When reared in environments with low food levels, forR larvae have higher survivorship and faster development than fors and fors2larvae. Together, these results show that natural variation in forhas far reaching implications affecting a suite of phenotypes involved in the regulation of food acquisition.
Spectral and spatial properties of polarized light reflections from the arms of squid (Loligo pealeii) and cuttlefish (Sepia officinalisL.)
Authors: Chiou Tsyr-Huei , Mäthger Lydia M. , Hanlon Roger T. , Cronin Thomas W. 
Published: October 2007

SUMMARYOn every arm of cuttlefish and squid there is a stripe of high-reflectance iridophores that reflects highly polarized light. Since cephalopods possess polarization vision, it has been hypothesized that these polarized stripes could serve an intraspecific communication function. We determined how polarization changes when these boneless arms move. By measuring the spectral and polarizing properties of the reflected light from samples at various angles of tilt and rotation, we found that the actual posture of the arm has little or no effect on partial polarization or the e-vector angle of the reflected light. However, when the illumination angle changed, the partial polarization of the reflected light also changed. The spectral reflections of the signals were also affected by the angle of illumination but not by the orientation of the sample. Electron microscope samples showed that these stripes are composed of several groups of multilayer platelets within the iridophores. The surface normal to each group is oriented at a different angle, which produces essentially constant reflection of polarized light over a range of viewing angles. These results demonstrate that cuttlefish and squid could send out reliable polarization signals to a receiver regardless of arm orientation.
A chymotrypsin-like serine protease interacts with the chitin synthase from the midgut of the tobacco hornworm
Authors: Broehan Gunnar , Zimoch Lars , Wessels Anton , Ertas Beyhan , Merzendorfer Hans 
Published: October 2007

SUMMARY
The chitin portion of the peritrophic matrix in the midgut of the tobacco hornworm, Manduca sexta, is produced by chitin synthase 2 (CHS2), a transmembrane family II glycosyltransferase, located at the apical tips of brush border microvilli. To look for proteins that potentially interact with CHS2, we performed yeast two-hybrid screening, identifying a novel chymotrypsin-like protease (CTLP1) that binds to the extracellular carboxyterminal domain of CHS2. The occurrence of this interaction in vivo is supported by co-localization and co-immunoprecipitation data. Based on our findings we propose that chitin synthesis is controlled by an intestinal proteolytic signalling cascade linking chitin synthase activity to the nutritional state of the larvae.
Sex and flow: the consequences of fluid shear for sperm–egg interactions
Authors: Riffell Jeffrey A. , Zimmer Richard K. 
Published: October 2007

SUMMARYFertilization is a complex interaction among biological traits of gametes and physical properties of the fluid environment. At the scale of fertilization (0.01–1 mm), sperm encounter eggs while being transported within a laminar (or viscous) shear flow. Varying laminar-shear in a Taylor-Couette flow tank, our experiments simulated important aspects of small-scale turbulence within the natural habitats of red abalone(Haliotis rufescens), a large marine mollusk and external fertilizer. Behavioral interactions between individual cells, sperm–egg encounter rates, and fertilization success were quantified, simultaneously, using a custom-built infrared laser and computer-assisted video imaging system. Relative to still water, sperm swam faster and moved towards an egg surface,but only in comparatively slow flows. Encounter rate, swim speed and orientation, and fertilization success each peaked at the lowest shear tested(0.1 s–1), and then decayed as shear increased beyond 1.0 s–1. The decay did not result, however, from damage to either sperm or eggs. Analytical and numerical models were used to estimate the propulsive force generated by sperm swimming (Fswim) and the shear force produced by fluid motion within the vicinity of a rotating egg(Fshear). To first order, male gametes were modeled as prolate spheroids. The ratio Fswim/Fshear was useful in explaining sperm–egg interactions. At low shears where Fswim/Fshear&gt;1, sperm swam towards eggs, encounter rates were pronounced, and fertilization success was very high; behavior overpowered fluid motion. In contrast, sperm swimming,encounter rate and fertilization success all decayed rapidly when Fswim/Fshear&lt;1; fluid motion dominated behavior. The shears maximizing fertilization success in the lab typically characterized natural flow microenvironments of spawning red abalone. Gamete behavior thus emerges as a critical determinant of sexual reproduction in the turbulent sea.
Male accessory glands of Drosophila melanogaster make a secreted angiotensin I-converting enzyme (ANCE), suggesting a role for the peptide-processing enzyme in seminal fluid
Authors: Rylett Caroline M. , Walker Michael J. , Howell Gareth J. , Shirras Alan D. , Isaac R. Elwyn 
Published: October 2007

SUMMARY
Angiotensin I-converting enzyme (ACE) expressed on the surface of endothelial cells is responsible for the last step in the synthesis of circulating angiotensin II and the inactivation of bradykinin. Mammalian ACE is also expressed in the prostate with other components of the renin–angiotensin system, and in developing spermatids, where the peptidase activity is known to be critical for normal sperm function. The importance of an ACE gene to male fertility has also been demonstrated in Drosophila melanogaster, where Ance is expressed in spermatids, and hypomorphic alleles of Ance cause a defect in spermiogenesis. Here we show that ANCE, which shares many enzymatic properties with mammalian ACE, is also a product of the male accessory gland of D. melanogaster. It is expressed in the secondary cells and is associated with the electron dense granule within the large vesicles of these cells. ACE proteolytic activity is lost from the accessory glands during mating,consistent with transfer to the mated female in the seminal fluid. The accessory gland ACE-like activity might have an evolutionarily conserved function processing biologically active peptides with a role in male fertility.
The acoustic mechanics of stick–slip friction in the California spiny lobster (Panulirus interruptus)
Authors: Patek S. N. , Baio J. E. 
Published: October 2007

SUMMARYThe dynamic interplay between static and sliding friction is fundamental to many animal movements. One interesting example of stick–slip friction is found in the sound-producing apparatus of many spiny lobster species(Palinuridae). The acoustic movements of the spiny lobster's plectrum over the file are generated by stick–slip friction between the two surfaces. We examined the microscopic anatomy, kinematics, acoustics and frictional properties of the California spiny lobster (Panulirus interruptus)toward the goal of quantitatively characterizing the frictional and acoustic mechanics of this system. Using synchronous high-speed video and sound recordings, we tested whether plectrum kinematics are correlated with acoustic signal features and found that plectrum velocity is positively correlated with acoustic amplitude. To characterize the frictional mechanics of the system, we measured frictional forces during sound production using excised plectrums and files. Similar to rubber materials sliding against hard surfaces, the static coefficient of friction in this system was on average 1.7. The change in the coefficient of friction across each stick–slip cycle varied substantially with an average change of 1.1. Although driven at a constant speed, the plectrum slipped at velocities that were positively correlated with the normal force between the two surfaces. Studies of friction in biological systems have focused primarily on adhesion and movement, while studies of stick–slip acoustics have remained under the purview of musical acoustics and engineering design. The present study offers an integrative analysis of an unusual bioacoustic mechanism and contrasts its physical parameters with other biological and engineered systems.