bluuebunny/crossref_metadata_2025 huggingface dataset:
Herbicide Programs for the Control of ALS-Resistant Shattercane (Sorghum bicolor) in Corn (Zea mays)
Authors: King Steven R. , Hagood Edward S.
Published: July 2006

Growers from three counties in Virginia have recently experienced difficulty controlling shattercane in corn with acetolactate synthase (ALS)–inhibiting herbicides. Seed was collected from these locations and from a susceptible biotype and tested for resistance to imazethapyr, imazapyr, and nicosulfuron in greenhouse trials. Seedlings from these locations were also treated with glufosinate and glyphosate. Greenhouse experiments indicated that one of the four shattercane biotypes was resistant to ALS-inhibiting herbicides. Effective control of the resistant biotype was possible with glufosinate or glyphosate. Field experiments were conducted in 2003 and 2004 to determine the most effective herbicide program utilizing herbicide-tolerant/-resistant corn hybrids for the control of shattercane. Early postemergence (EP) and late postemergence (LP) applications of imazethapyr plus imazapyr or EP nicosulfuron did not control shattercane, and yield from the imidazolinone-tolerant (IT) hybrid was equivalent between these treatments and was equivalent to yield from the weedy control (WC). At 23 wk after planting (WAP), EP applications of glyphosate controlled shattercane 71 and 75% compared to only 21 and 66% with EP applications of glufosinate in 2003 and 2004, respectively. In both years, LP applications of glufosinate or glyphosate controlled shattercane better than did EP applications of glufosinate or glyphosate. Treatment timing with respect to corn yield within either the glufosinate-resistant (LL) or glyphosate-resistant (RR) corn hybrid was critical. EP treatments of glufosinate or glyphosate resulted in yields that were equivalent to yield from the weed-free control (WFC) of each hybrid. LP treatments of glufosinate or glyphosate, however, resulted in yields that were equivalent to only 90 and 91% of yield from the WFC of each hybrid, respectively.
Evaluating the Economic Risk of Herbicide-Based Weed Management Systems in Corn and Soybean Using Stochastic Dominance Testing
Authors: Hoverstad Thomas R. , Johnson Gregg A. , Gunsolus Jeffrey L. , King Robert P.
Published: July 2006

Herbicide evaluation trials are typically conducted with the objective of rating herbicide efficacy and assessing crop yield loss. There is little if any attempt to quantify the economic risk associated with each treatment. The objective of this research was to use second-degree stochastic dominance to evaluate the economic stability of corn and soybean weed management systems between two contrasting environments. Weed management systems were evaluated in small-plot replicated trials over a 3-yr time period at two locations in southern Minnesota. One location (Waseca) had a slightly cooler and wetter environment than the second location (Lamberton). The Waseca location also had higher weed density and greater weed species diversity. Adjusted returns from weed management were calculated for each system by measuring economic returns, as determined by deducting weed management costs from the product of crop price and grain yield. Stochastic dominance is a technique that considers the entire distribution of net returns from weed management and compares these cumulative distributions as a basis for analyzing risk. Climate, soils, and weed diversity dictated differences in risk efficiency and effectiveness of the various weed management systems evaluated between the Waseca and Lamberton sites. Stochastic dominance testing is a useful tool for understanding long-term risk across environments. Results can be used to develop effective long-term weed management systems that minimize risk while maximizing profit potential.
Control of Volunteer Canola with Herbicides: Effects of Plant Growth Stage and Cold Acclimation
Authors: Légère Anne , Simard Marie-Josée , Johnson Eric , Stevenson F. Craig , Beckie Hugh , Blackshaw Robert E.
Published: July 2006

Phenoxy herbicides are frequently used to control volunteer canola populations. However, there have been claims that poor control could be due to cold acclimation of canola plants in the spring. The objective of this study was to determine whether cold acclimation or growth stage affected the response of canola volunteers to herbicides. In a growth room experiment, canola plants were prehardened and cold acclimated or were grown at 20/12 C and treated with one of six 2,4-D doses. Cold acclimation as achieved by this experiment affected upper and lower asymptotes of the dose–response curve but not the herbicide dose required to reduce canola weight by 50% relative to the nontreated control (GR50), indicating limited cold-related effects on canola tolerance to 2,4-D. Field experiments, conducted in the provinces of Québec and Saskatchewan, examined the effects of canola growth stage on the efficacy of 2,4-D, MCPA, and carfentrazone. Comparisons of the estimates from the dose–response curves confirmed that herbicide efficacy was consistently greater when canola plants were treated at an early growth stage, regardless of cultivar or herbicide used. The GR50estimates for canola plants treated at a later growth stage exceeded the recommended rates. Some canola plants grown as volunteers in a wheat crop survived 2,4-D or MCPA treatments at 0.5× and 1× rates and produced up to 148 seeds/m2. Efficient control of canola volunteers will be obtained when plants are sprayed at an early growth stage, but near-total control will be highly desirable in order to restrict seedbank buildup, particularly when dealing with canola cultivars with different herbicide-resistant traits.
Tolerance of a Glyphosate-Resistant Soybean to Late-Season Glyphosate Applications
Authors: Norsworthy Jason K.
Published: July 2006

Tolerance and yield of ‘H8001 RR’ soybean to single and sequential glyphosate applications made during vegetative and reproductive stages were examined in field trials in 2000 and 2001. In addition, germination and seedling characteristics from harvested seed were assessed. Glyphosate-resistant soybean tolerated single and sequential applications of 1.7 kg ae/ha glyphosate with minimal injury (≤5%), except for an R2 application in 2000 that caused 20% injury. All observed injury was transient and did not adversely affect soybean density, height, seed weight, or seed yield. Germination and seedling growth of harvested seed were similar to those of a nontreated control. These results suggest that glyphosate-resistant soybean can withstand sequential applications of glyphosate during vegetative and reproductive stages without prolonged adverse effects.
Fission-track thermochronology of the Oman Mountains continental windows, and current problems of tectonic interpretation
Authors: Saddiqi Omar , Michard André , Goffe Bruno , Poupeau Gérard , Oberhänsli Roland
Published: July 2006

The Oman Mountain belt offers a unique case study of an Alpine orogen where blueschist- and eclogite-facies metamorphism developed in continental rocks beneath an ophiolite in the absence of continental collision. We present hereafter the first systematic, fission-track (FT) study of the subophiolitic Jebel Akhdar and Saih Hatat windows in the central-southern Oman Mountains. Nineteen samples out of 28 yielded significant zircon and/or apatite FT results. All of the 9 samples from NE (internal) Saih Hatat, where metamorphism occurred at ca. 300°C < T < 550°C (low-grade blueschist to low-grade eclogite facies), yielded FT zircon ages at 66-70 Ma. Four samples from SW Saih Hatat (front of the Fe-Mg carpholite zone, ca. 280°C < T < 300°C) yielded 69-93 Ma dates, and 4 samples from Jebel Akhdar (ca. 250°C < T < 280°C) yielded 80-96 Ma dates, which reflects partial resetting of the zircon FT chronometre at T ≤ ca. 280°C. As eclogite metamorphism of the deepest Saih Hatat units is dated at ca. 80 Ma [Warren et al., 2003], we deduce an early cooling rate of 30°C/Ma for these units. Late thermal evolution is constrained by apatite FT length optimization analysis and includes, i) cooling under 60°C until 60-58 Ma (rate close to 10°C/Ma); and ii) heating over 80°C at ca. 20-8 Ma.

The Oman Mountains tectonic building is currently accounted for by contrasting models involving one or two subductions. Taking into account the structural and geophysical data on the Saih Hatat metamorphic pile, we interpret the reported thermal evolution in the framework of the classical, one subduction model: i) Permian rifting and Mesozoic spreading; ii) late Cretaceous intra-oceanic subduction followed by continental margin subduction/ophiolite obduction; iii) late Late Cretaceous-Paleocene synorogenic exhumation of the subducted units through extrusion within the subduction channel (relative extension), then isostatic rebound and extensional inversion of the obduction thrust; and iv) Neogene compression resulting in rejuvenation of the basal thrust beneath the continental windows, which are considered to be parautochthonous.
The Tunissian “zone des nappes”: a slightly inverted mesocenozoic continental margin (Taberka/Jendouba; northwestern Tunisia)
Authors: Ould Bagga Mohamed Abdoullah , Abdeljaouad Saâdi , Mercier Eric
Published: July 2006

Detailed investigations in the western part of the “zone des nappes” in the Tunisian Atlas enable to propose an original model for this area. We show that, according to sedimentary records, these units appear to be formed by various series originally deposited on tilted crustal blocks of the North African margin. This south-easternward tilting occurred from the Triasic to the early Miocene. The first phase of inversion took place during the early to middle Miocene interval; no older compressive event can be highlighted. The shortening is associated with a system of flats and ramps thrust faults that occurs following a piggy-back sequence and that does not disrupt the paleogeographic order. Subsequently, an “out-of-sequence” event places the upper unit (Numidian Unit) onto the sub-numidian Units. The overlap length remains very moderate betwen sub-numidian Units (a few kilometers only). Finally, during the late Quaternary, the area undergoes a late shortening that folds the syn-tectonic basins.
The Length of the Spermatogenic Cycle Is Conserved in Porcine and Ovine Testis Xenografts
Authors: Zeng Wenxian , Avelar Gleide F. , Rathi Rahul , Franca Luiz R. , Dobrinski Ina
Published: July 2006

ABSTRACT: Xenografting of immature mammalian testis tissue into mice can accelerate sperm production. To determine whether this shortened time to sperm production is because of reduced length of the spermatogenic cycle, we applied bromodeoxyuridine (BrdU) incorporation to analyze the spermatogenic cycle in porcine and ovine testis xenografts. Small testis fragments from newborn pigs and sheep were ectopically grafted into mice. Once complete spermatogenesis was present in grafted tissue, mice were injected with BrdU and grafts were recovered at different time points thereafter. In porcine grafts, the most advanced germ cells labeled 1 hour, 9 days, 12.3 days, and 18 days after BrdU injection were stage 1 preleptotene/leptotene primary spermatocytes, stage 1 pachytene primary spermatocytes, stage 5 newly‐formed round spermatids, and late stage 2 elongating spermatids, respectively. In ovine grafts, the most advanced labeled germ cells at 1 hour, 11 days, and 22 days post‐BrdU injection were stage 2 preleptotene/leptotene primary spermatocytes, late stage 1 pachytene primary spermatocytes, and stage 2 elongating spermatids, respectively. These results indicate that each spermatogenic cycle in porcine and ovine xenografts lasts approximately 9 and 11 days, respectively, which is similar to their durations in situ. Therefore, the length of the spermatogenic cycle is conserved in porcine and ovine testis xenografts. This is consistent with earlier reports showing that the cycle length is inherent to the germ cell genotype. The shortened time to sperm production in xenografts therefore appears attributable to accelerated maturation of the testicular somatic compartments. Our results suggest that testis xenografts provide a useful model to study the timing of testicular maturation and spermatogenesis in different mammalian species.
Dose—Response Relationship Between Testosterone and Erectile Function: Evidence for the Existence of a Critical Threshold
Authors: Armagan Abdullah , Kim Noel N. , Goldstein Irwin , Traish Abdulmaged M.
Published: July 2006

ABSTRACT:Androgens play an important role in erectile function. However, the dose—response relationship between plasma testosterone levels and penile erection remains unclear. Intact (sham operated) or bilaterally orchiectomized, mature male Sprague‐Dawley rats were used. Two weeks after surgery, rats were infused continuously with either vehicle (polyethyleneglycol) or varying doses of testosterone (44, 88, 220, or 440 μg/day) for 14 days using subcutaneous osmotic infusion pumps (study 1). In a separate study, 4 weeks after surgery, rats were infused with a lower range of testosterone doses (11, 22, or 44 μg/day) for 14 days (study 2). In the first study, intact rats had a mean plasma testosterone concentration of 0.56 ± 0.12 ng/mL (∼1.9 nM), as determined by standard radioimmunoassay. In the second study, a more sensitive enzyme‐linked immunoassay was used to measure the lower testosterone levels. Using this assay, intact rats had a mean plasma testosterone concentration of 2.02 ± 0.59 ng/mL. Intracavernosal pressure measurements indicated that orchiectomy resulted in a significant reduction in erectile function, when compared to intact animals, whereas testosterone infusion restored erectile function to varying degrees. Erectile function was maintained by a wide range of systemic testosterone levels as low as 10%–12% of normal physiological plasma concentrations. Below these concentrations, erectile function was significantly and positively correlated with testosterone plasma levels in a dose‐dependent manner. Interestingly, prostate tissue mass was positively correlated to plasma testosterone levels across all concentrations examined. Protein expression of neural nitric oxide synthase (nNOS) and phosphodiesterase type 5 (PDE 5) was reduced in penile tissue from orchiectomized animals and increased in testosterone‐infused animals, as assessed by Western blot analyses. We suggest that testosterone at levels approaching one‐tenth normal physiological plasma concentration may represent a threshold value, below which erectile function declines in a dose‐dependent fashion. However, different androgen‐dependent tissues may exhibit varying sensitivities to circulating testosterone with regard to growth and function.
Testis‐Specific Lactate Dehydrogenase (LDH‐C4; Ldh3) in Murine Oocytes and Preimplantation Embryos
Authors: Coonrod Scott , Vitale Alejandra , Duan Chongwen , Bristol‐Gould Sarah , Herr John , Goldberg Erwin
Published: July 2006

ABSTRACT: LDH‐C4 (Ldh3) is a member of the lactate dehydrogenase family of isozymes that catalyze the terminal reaction in the glycolytic pathway. In mammals, 3 genes, ldha, ldhb, and Ldhc, encode the subunits that assemble into catalytically active homo‐ and heterotetramers. Differential expression of these genes determines the lactate dehydrogenase (LDH) isozyme composition of tissues, and, as is well known, A subunits predominate in skeletal muscle and B subunits are abundantly produced in brain and heart, with the Ldh2 isozyme the most abundant form in oocytes. The C peptide can be detected first in pachytene spermatocytes and constitutes the primary LDH of spermatozoa. Originally the Ldhc gene (Ldh3 in terminology applied to murine cells) was considered to be testis specific on the basis of immunochemical, enzymatic, and molecular analyses. Here we report the detection of this isozyme in the murine oocyte and early embryo. Our results indicate that Ldh3 mRNA is transcribed in oocytes and cannot be detected in fertilized eggs. Ldh3 protein, however, persists to the blastocyst stage of embryonic development localizing mainly to the cortex region of oocytes, eggs, zygotes, and embryonic blastomeres.
Inhibin‐B Levels in Healthy Young Adult Men and Prepubertal Boys: Is Obesity the Cause for the Contemporary Decline in Sperm Count Because of Fewer Sertoli Cells?
Authors: Winters Stephen J. , Wang Chenxi , Abdelrahaman Eiman , Hadeed Venus , Dyky Mary Ann , Brufsky Adam
Published: July 2006

ABSTRACT: Inhibin‐B is a heterodimeric glycoprotein produced by Sertoli cells. Although inhibin‐B levels are low when seminiferous tubules are damaged, studies in normal monkeys reveal that inhibin‐B levels also correlate positively with Sertoli cell number. In this study, we measured inhibin‐B levels in healthy young adult men aged 18–24 years and in prepubertal boys aged 5–9 years in relation to body mass index (BMI). Inhibin‐B levels declined with increasing obesity in young adult men; values were 26% lower in men who were obese compared to normal‐weight men. Sex hormone—binding globulin and total testosterone, but not free testosterone, were also lower with increasing BMI; serum follicle‐stimulating hormone and luteinizing hormone levels were unaffected by obesity. In prepubertal boys, by contrast, inhibin‐B was unaffected by obesity. We propose that reduced levels of inhibin‐B indicate that obese men have fewer Sertoli cells than men of normal weight. Moreover, normal values in obese prepubertal boys suggest that the effect of obesity on inhibin‐B is established during puberty. Finally, because each Sertoli cell is thought to support a finite number of germ cells, fewer Sertoli cells in obesity may predispose to a lower sperm count in adulthood. We speculate that the escalating prevalence of obesity and insulin resistance among adolescents might negatively influence male reproductive function for the next generation.
Proteins of the Cauda Epididymal Fluid Associated With Fertility of Mature Dairy Bulls
Authors: Moura Arlindo A. , Chapman David A. , Koc Hasan , Killian Gary J.
Published: July 2006

ABSTRACT: We evaluated the relationships between proteins in cauda epididymis fluid (CEF) and fertility scores of dairy bulls. Fertility was expressed as the percentage point deviation (PD) of bull nonreturn rate from the average fertility of all bulls at an artificial insemination center. The number of services for each bull ranged from 1074 to 52 820, and PD values ranged from +7.7% to −6.6%. CEF from 20 bulls was obtained from vasa deferentia cannulae and was separated from sperm by centrifugation immediately after collection. Samples were evaluated by 2‐dimensional (2‐D) sodium dodecyl sulfate polyacrylamide gel electrophoresis gels stained with Coomassie blue, and polypeptide maps were analyzed by PDQuest software. Protein quantities, defined as the total integrated optical density of the spots, were compared between groups of high‐fertility sires (n = 12; PD ≥ 0) and low‐fertility sires (n = 8; PD < 0) and were also used as independent variables in regression analysis. Proteins were identified by capillary liquid chromatography—nanoelectrospray ionization—tandem mass spectrometry. An average of 118 spots was detected in 2‐D maps of the CEF, but we were unable to distinguish any protein that was expressed only in high‐fertility or in low‐fertility bulls. However, the amount of α‐L‐fucosidase 2 and cathepsin D was 2.3‐ and 2.4‐fold greater (P < .05) in high‐fertility than in low‐fertility bulls, respectively. Conversely, the intensities of 3 isoforms (24–27 kd; pl 6.3–5.8) of prostaglandin D‐synthase (PGDS) were from 3.2‐ to 2.2‐fold greater in low‐fertility sires (P < .05). An empirical regression model established that a significant proportion (R2 = 0.72; P < .0001) of the variation in fertility scores (PD values) was explained by the intensities of cathepsin D and 1 isoform of PGDS (24 kd; pl 6.3). Thus, multiple proteins present in the CEF are potential biomarkers of fertility in high‐use, mature Holstein bulls.
De Novo Morphogenesis of Seminiferous Tubules From Dissociated Immature Rat Testicular Cells in Xenografts
Authors: Gassei Kathrin , Schlatt Stefan , Ehmcke Jens
Published: July 2006

ABSTRACT: Testicular development is initiated with the differentiation of Sertoli cells in the embryonic gonad. The aggregation of Sertoli cells is crucial for the generation of testicular cords and thus for the first sign of male gonadal development. To date, functional testicular tissue has not yet been generated in vitro. The objective of this study was to explore the de novo morphogenesis of testicular tissue from isolated postnatal rat testicular cells using a combination of in vitro culture and ectopic xenografting. Immature rat testicular cells were cultured in either a 2‐dimensional (laminin‐coated coverglass) or a 3‐dimensional (extracellular matrix gel) culture system. Whereas testicular cells cultured on laminin showed a slow morphogenetic cascade resulting in cord formation after about 10 days of culture, cells cultured on extracellular matrix gel assembled to a network of cordlike structures within several hours after plating and formed spherical cell aggregates at day 3. Further progression of the morphogenetic cascade was not obtained in either the 2‐ or the 3‐dimensional culture system. In contrast, structures resembling immature testicular tissue were obtained after xenografting of extracellular matrix gel—enclosed spherical testicular cell aggregates. The grafts were vascularized and contained elongated seminiferous tubules. Histologic analysis revealed the presence of a basement membrane, a histologically normal interstitium containing putative Leydig cells, the establishment of tubule lumen, and the integration of few putative spermatogonia into the seminiferous epithelium. We conclude that immature rat testicular cells carry the full potential to generate all somatic components of a testis in xenografts, thus opening fascinating pathways to study testicular organogenesis.
A New Analytical Tire Model for Cornering Simulation. Part I: Cornering Power and Self-Aligning Torque Power
Authors: Kabe K. , Miyashita N.
Published: July 2006

A new analytical tire model for cornering power (CP) and self-aligning torque power (SATP) is proposed on the basis of the Fiala model. In a pneumatic tire, the self-deformation by the transmission of force and torque is so large to influence recursively the force and torque generation during cornering. Then CP and SATP have negative feedback loops: As CP and SATP increase, the steering transmission loss by the tire self-deformation also increases to depress further increments of CP and SATP. The present model, the CP∕SATP system model, analytically describes the force and torque transmission with feedback loops by taking into account not only (i) the shear deformation of the tread rubber and (ii) the in-plane belt deflection, but also (iii) the out-of-plane sidewall rotation. As well as other practical systems with a negative feedback loop, the CP and SATP feedback stabilize the CP and SATP output level at a higher vertical load, and approximates the measured load dependence of CP and SATP with high accuracy. Although the sidewall rotation feedback by SATP has not been considered in conventional cornering studies, its contribution in recent radial tires is shown to be larger than that of belt deflection by CP. The model is applicable to not only the numerical simulation for tire design but also the inverse data analysis of the cornering test. Nonlinear least-squares fittings of the measured data to the model are excellent and give the dynamic estimates of tire-part stiffness.
Reducing Tire-Induced Noise and Vibration
Authors: Yilmaz C. , Hulbert G. M. , Kikuchi N.
Published: July 2006

Tire-induced noise and vibration spans a wide range of frequencies, depending on, among other attributes, tread design, road surface, and vehicle speed. Vehicle designers are faced with the daunting task of minimizing this broad frequency of energy. The design of suspension systems must take into account the need to have a well-tuned frequency response.

In this paper, a new approach toward minimizing tire-induced noise and vibration is presented. The methodology is based upon a new perspective of employing antiresonance, as opposed to damping phenomena, to effectively tune systems for practical performance. The mechanical structure of the system is amenable to cost-effective manufacture and can be packaged in different configurations. We present the fundamental approach toward the design and give several example configurations.
The Behavior of Carbon Black-Filled Natural Rubber under High Strain Rates
Authors: Hussain Syeda A. , Fatt Michelle S. Hoo
Published: July 2006

Tensile tests were conducted to obtain the deformation and failure characteristics of unfilled natural rubber (NR) and natural rubber with 25, 50, and 75 phr of N550 carbon black filler under quasistatic and dynamic loading conditions. The quasistatic tests were performed on an electromechanical INSTRON machine, while the dynamic test data were obtained from tensile impact experiments using a Charpy impact apparatus. In general, the modulus of the stress-extension ratio curves increases with increasing strain rate up to about 407, 367, 346, and 360 s−1 for unfilled, and 25, 50, and 75 phr for filled NR, respectively. Above these strain rates, the unfilled and filled natural rubber stress-extension ratio curves remained unchanged. The modulus increased with increasing strain rate because there was little time for stress relaxation. Above a critical strain rate, no change in modulus was observed because the time of the experiment was short compared to the lowest characteristic relaxation time of the material. Dynamic stress-extension ratio curves did not have the very sharp upturn at break, which is observed from strain-induced crystallization in natural rubber under quasistatic loading. Strain-induced crystallization appeared to be suppressed at high rates of loading. In fact, the highest dynamic tensile strength for the 25- and 50-phr carbon black-filled natural rubbers was smaller than those under quasistatic loading, while the highest dynamic tensile strength of the 75-phr carbon black-filled NR was greater than that in the static test. This indicated that high amounts of carbon black fillers will impede strain-induced crystallization in natural rubber.
Cell‐type‐specific regulation of RNA polymerase I transcription: a new frontier
Authors: Tseng Hung
Published: July 2006

Ribosomal RNA transcription was one of the first model systems for molecular characterization of a transcription regulatory mechanism and certainly one of the best studied in the widest range of organisms. In multicellular organisms, however, the issue of cell‐type‐specific regulation of rRNA transcription has not been well addressed. Here I propose that a systematic study of cell‐type‐specific regulation of rRNA transcription may reveal new regulatory mechanisms that have not been previously realized. Specifically, issues concerning the cell‐type‐specific requirement for rRNA production, the universality of Pol I transcription complex and the division of rDNA into regulatory subdomains are discussed. BioEssays 28: 719–725, 2006. © 2006 Wiley Periodicals, Inc.
Origin and evolution of the vertebrate vomeronasal system viewed through system‐specific genes
Authors: Grus Wendy E. , Zhang Jianzhi
Published: July 2006

Tetrapods have two distinct nasal chemosensory systems, the main olfactory system and the vomeronasal system (VNS). Defined by certain morphological components, the main olfactory system is present in all groups of vertebrates, while the VNS is found only in tetrapods. Previous attempts to identify a VNS precursor in teleost fish were limited by functional and morphological characters that could not clearly distinguish between homologous and analogous systems. In the past decade, several genes that specifically function in the VNS have been discovered. Here we first describe recent evolutionary studies of mammalian VNS‐specific genes. We then review evidence showing the presence and tissue‐specific expression of the VNS‐specific genes in teleosts, as well as co‐expression patterns of these genes in specific regions of the teleost olfactory epithelium. We propose that a VNS precursor exists in teleosts and that its evolutionary origin predated the separation between teleosts and tetrapods. BioEssays 28: 709–718, 2006. © 2006 Wiley Periodicals, Inc.
The effect of GeneChip gene definitions on the microarray study of cancers
Authors: Lu Xuesong , Zhang Xuegong
Published: July 2006

The Affymetrix GeneChip is a popular microarray platform for genome‐wide expression profiling and has been widely used in functional genomics especially in the classification of cancers. Due to the updating of genome data, much of the genome information with which the chips were designed is out‐of‐date and it has been reported that many of the genes/transcripts on the chips differ from their original definition when mapping the probes to the new genome information. Dai et al. have reported that the updated definition can cause as much as 30–50% discrepancy in the genes selected as differentially expressed on a heart tissue expression profiling dataset. Understanding the nature of this difference is therefore very important for the utilization of the data. In this work, with a large cancer dataset as an example, we compared two major definitions and investigated their effects on classification, clustering, discovery of differentially expressed genes and gene‐set‐based analysis. Results show that the two definitions agree well on clustering and classification results but genes and gene sets discovered as differentially expressed or enriched can be very different. Discoveries based on the Affymetrix definition can cover most of those based on the new definition, but tend to have more false positives. BioEssays 28: 739–746, 2006. © 2006 Wiley Periodicals, Inc.
Measuring cooperativity in the formation of a three‐stranded β sheet (double hairpin)
Authors: Hudson F. Michael , Andersen Niels H.
Published: July 2006

Recently validated chemical shift measures of hairpin structuring have been applied to a series of turn mutants of the Schenck–Gellman three‐strand β‐sheet model with the aim of measuring the entropic advantage associated with aligning an additional strand onto an existing hairpin versus aligning the same two strands in an initial hairpin formation. In a four‐state analysis (unfolded, 2 single hairpins, and the double hairpin fold in equilibrium) a cooperativity index can be defined as the factor by which the equilibrium constant for hairpin formation is improved when one strand is prestructured. This cooperativity index is 2.7 ± 0.7 for hairpin formation about a stable D‐Pro‐Gly turn locus and increases to 7.6 ± 1.2 for an Asn‐Gly turn locus. The latter corresponds to a cooperativity induced ΔΔG increment of 4.9 kJ/mol for the folding of a hairpin. Although larger than previous experimental measures of folding cooperativity in three‐stranded sheets, the magnitude of this effect (which is considerably less than the TΔΔS expectation for prestructuring three or more β‐strand residue sites) likely reflects the intrinsic preference of these designed sequences for extended conformations. If similar or larger effects apply to protein β‐sheet folding, it is not surprising that particularly favorable hairpin alignments serve as nucleation sites in protein folding pathways. © 2006 Wiley Periodicals, Inc. Biopolymers 83:424–433, 2006

This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Fabrication of agar‐gelatin hybrid scaffolds using a novel entrapment method for in vitro tissue engineering applications
Authors: Verma Vipin , Verma Poonam , Kar Santosh , Ray Pratima , Ray Alok R.
Published: July 2006

Scaffolds of agar and gelatin were developed using a novel entrapment method where agar and gelatin molecules mutually entrapped one another forming stable cell adhesive matrices. Glutaraldehyde was used as a crosslinking agent for gelatin. Three types of hybrid matrices were prepared using agar and gelatin in different proportions in the weight ratio of 1:1, 2:1, and 3:1. Surface characterization of dry scaffolds was carried out by scanning electron microscope. Swelling studies were carried out in phosphate buffer saline (PBS) at physiological pH 7.4. The integral stability of the scaffolds was evaluated by estimating the released disintegrated gelatin from them in PBS at pH 7.4. The attachment kinetics of the cells was evaluated by culturing mouse fibroblast cell line NIH 3T3 on films. The cytocompatibility of these matrices was determined by studying growth kinetics of NIH 3T3 cells on them and morphology of cells was observed through optical photographs taken at various days of culture. It was found that the matrices containing agar and gelatin in 2:1 weight ratio exhibited best growth kinetics. The results obtained from these studies have suggested that the above‐described method is a cheap and easy way to fabricate agar‐gelatin hybrid scaffolds to grow cells which can be used in various in vitro tissue engineering applications like screening of drugs. Biotechnol. Bioeng. 2007;96: 392–400. © 2006 Wiley Periodicals, Inc.
Synthesis and Characterization of Nonconventional Surfactants of Aromatic Amino Acid–Glycerol Ethers: Effect of the Amino Acid Moiety on the Orientation and Surface Properties of These Soap‐Type Amphiphiles
Authors: Varka Evdoxia‐Maria A. , Heli Maria G. , Coutouli‐Argyropoulou Evdoxia , Pegiadou Sofia A.
Published: July 2006

The synthesis, characterization, and surface properties of soap‐type amphiphiles comprising alkyl chains of 10–16 carbon atoms linked through an ether group to a glycerol–amino acid hydrophilic head group is described. The surface properties of members of this series derived from histidine and tyrosine were compared with those of phenylalanine and tryptophan derivatives described previously and with those of conventional soaps. In all cases, the amino acid derivatives showed superior surface properties, and an interesting differentiation was discovered regarding the orientation of tryptophan derivatives.
Homo‐ and Heteropolynuclear Platinum Complexes Stabilized by Dimethylpyrazolato and Alkynyl Bridging Ligands: Synthesis, Structures, and Luminescence
Authors: Forniés Juan , Fuertes Sara , Martín Antonio , Sicilia Violeta , Lalinde Elena , Moreno M. Teresa
Published: July 2006

This work describes the synthesis of cis‐[Pt(CCPh)2(Hdmpz)2] (1) and its use as a precursor for the preparation of homo‐ and heteropolynuclear complexes. Double deprotonation of compound 1 with readily available MI (M = Cu, Ag, Au) or MII (M = Pd, Pt) species affords the discrete hexanuclear clusters [{PtM2(μ‐CCPh)2(μ‐dmpz)2}2] [M = Cu (2), Ag (3), Au (4)], in which both “Pt(CCPh)2(dmpz)2” fragments are connected by four d10 metal centers, and are stabilized by alkynyl and dimethylpyrazolate bridging ligands, or the trinuclear complexes [Pt(μ‐CCPh)2(μ‐dmpz)2{M(C∧P)}2] (M = Pd (5), Pt (6); C∧P = CH2‐C6H4‐P(o‐tolyl)2‐κC,P), respectively. The X‐ray structures of complexes 1–4 and 6 are reported. The X‐ray structure of the platinum–copper derivative 2 shows that all copper centers exhibit similar local geometry being linearly coordinated to a nitrogen atom and η2 to one alkynyl fragment. However in the related platinum–silver (3) and platinum–gold (4) derivatives the silver and gold atoms present three different coordination environments. The complexes have been studied by absorption and emission spectroscopy. The hexanuclear complexes exhibit bright luminescence in the solid state and in fluid solution (except 4 in the solid state at 298 K). Dual long‐lived emission is observed, being clearly resolved in low‐temperature rigid media. The low‐energy emission is ascribed to MLM′CT Pt(d)/π(CCPh)→Pt(pz)/M′(sp)/π*(CCPh) modified by metal–metal interactions whereas the high‐energy emission is tentatively attributed to an emissive state derived from dimethylpyrazolate‐to‐metal (d10) LM′CT transitions π(dmpz)→M′(d10).
Multicomponent Synthesis of Dihydropyrimidines and Thiazines
Authors: Vugts Danielle J. , Koningstein Manoe M. , Schmitz Rob F. , de Kanter Frans J. J. , Groen Marinus B. , Orru Romano V. A.
Published: July 2006

A broad range of differently substituted dihydropyrimidines and thiazines can be efficiently prepared by using a four‐component reaction between phosphonates, nitriles, aldehydes, and iso(thio)cyanates. The scope and limitations of this multicomponent reaction are fully described. Variation of all four components has been investigated. The nitrile and aldehyde inputs can be varied extensively, but variation of the phosphonate input remains limited. An interesting rearrangement leading to phosphoramidates has been observed. Furthermore, the multicomponent reaction seems to be restricted to the use of isocyanates with strongly electron‐withdrawing substituents, but an interesting additional exchange reaction under microwave conditions leads to dihydropyrimidines with less electron‐withdrawing substituents at N3. In addition, a diastereoselective formation of dihydropyrimidines has been observed when using a chiral aldehyde as the input. Finally, by changing the isocyanate component to an isothiocyanate, thiazines are efficiently formed instead of the corresponding thio‐dihydropyrimidines.
A Novel Method for the In Situ Determination of Concentration Gradients in the Electrolyte of Li‐Ion Batteries
Authors: Zhou Jiang , Danilov Dmitry , Notten Peter H. L.
Published: July 2006

An electrochemical method has been developed for the in situ determination of concentration gradients in the electrolyte of sealed Li‐ion batteries by measuring the potential difference between microreference electrodes. Formulas relating the concentration gradient and the potential difference between the microreference electrodes were derived from the Nernst–Planck equation. The concentration gradients in Li‐ion batteries are theoretically and experimentally proven to be linear at steady state under galvanostatic charging and discharging conditions. Based on this finding, both the diffusion coefficient of the lithium ions in the electrolyte and the diffusion overpotential related to the concentration gradient have been calculated. It was found that the concentration gradient is proportional to the applied current over a wide current range and that the obtained diffusion coefficient of lithium ions is almost constant. For the batteries studied in this work, the diffusion overpotential is already noticeable at 0.30 A and the limiting current is estimated to be 1.1 A, corresponding to a C‐rate of 3.7.
Persilylated Phosphoranyl Radicals: The First Persistent Noncyclic Phosphoranyl Radicals
Authors: Berchadsky Yves , Bernard‐Henriet Christiane , Finet Jean‐Pierre , Lauricella Robert , Marque Sylvain R. A. , Tordo Paul
Published: July 2006

Persistent noncyclic phosphoranyl radicals have been prepared and observed by electron paramagnetic resonance (EPR) for the first time. They were obtained by UV‐photolysis of a solution containing a bis(trialkylsilyl) peroxide (R = Me, Et) and a tris(trialkylsilyl) phosphite (R = Me, Et, iPr). EPR parameters (aP ≈ 100 mT) are typical of phosphoranyl radicals exhibiting a trigonal‐bipyramidal structure, with the odd electron in an equatorial site. Analysis of the pseudo‐first‐order decay shows that these phosphoranyl radicals decay by SH2 homolytic substitution on the bis(trialkylsilyl) peroxide and by loss of a trialkylsilyloxyl radical (α‐scission reaction). Both the SH2 and α‐scission reactions depend on the steric bulk of the alkyl groups, that is, the bulkier the alkyl group, the slower the SH2 and α‐scission reactions.
Methylazacalixpyridines: Remarkable Bridging Nitrogen‐Tuned Conformations and Cavities with Unique Recognition Properties
Authors: Gong Han‐Yuan , Zhang Xiao‐Hang , Wang De‐Xian , Ma Hong‐Wei , Zheng Qi‐Yu , Wang Mei‐Xiang
Published: July 2006

Methylazacalix[n]pyridines (n = 4, 8) and methylazacalix[m]arene[n]pyridines (m = n = 2, 4) have been synthesized by a convenient fragment coupling approach starting from 2,6‐dibromopyridine, 2,6‐diaminopyridine, and benzene‐1,3‐diamine. Thanks to the intrinsic electronic nature of nitrogen, which can adopt mainly sp2 hybridization, allowing it variously to conjugate, partially conjugate, or not conjugate with the adjacent one or two pyridine rings, the resulting nitrogen‐bridged calixpyridine derivatives act as a unique class of macrocyclic host molecules with intriguing conformational structures offering fine‐tunable cavities and versatile recognition properties. Whilst in solution it is fluxional, in the solid state methylazacalix[4]pyridine adopts a 1,3‐alternate conformation with a C2v symmetry in which every two bridging nitrogen atoms conjugate with one pyridine ring. After protonation, the methylazacalix[4]pyridinium species has a different conjugation system of its four bridging nitrogen atoms, yielding the similar twisted 1,3‐alternate conformations with an approximate S4 symmetry. The cavity of each protonated methylazacalix[4]pyridine, however, varies finely to accommodate guest species of different size and geometry, such as planar DMF or HO2CCO2− ion, a twisted HO2CCO2− ion, and a tetrahedral ClO4− ion. As giant macrocyclic hosts, both methylazacalix[8]pyridine and methylazacalix[4]arene[4]pyridine interact efficiently with fullerenes C60 and C70 through van der Waals forces. Their ease of preparation, versatile conformational structures, and recognition properties make these multinitrogen‐containing calixarenes or cyclophanes unique and powerful macrocyclic hosts in supramolecular chemistry.
Gastrodin Interaction with Human Fibrinogen: Anticoagulant Effects and Binding Studies
Authors: Liu Yang , Tang Xiaoling , Pei Jianfeng , Zhang Li , Liu Feng , Li Ke'an
Published: July 2006

In an effort to identify the anticoagulant activity of gastrodin (GAS) and to investigate the possibility of its use as a novel anticoagulant drug, the binding characteristics of GAS to human fibrinogen (Fg) were studied by using a quartz crystal microbalance (QCM) biosensor, anticoagulant animal experiments, and a molecular docking simulation. Real‐time kinetic analysis with the QCM biosensor revealed that the in vitro binding of GAS to Fg was strong under physiological ionic conditions as the determined equilibrium dissociation constant (KD) was 1.94×10−6 M. To check whether this strong binding may influence the natural coagulation function of Fg, the in vivo effect of GAS on the coagulation system of rats was examined. The results showed that GAS can significantly prolong the coagulation time (CT) and decrease the Fg content, while it had no effect on the activated kaolin partial thromboplastin time (KPTT) or prothrombin time (PT) in rats. To clarify the mechanism of the specific interaction, a molecular docking simulation was also performed to provide reasonable binding models for the interaction of GAS with Fg at the atomic level. GAS binds strongly to the inherent polymerization sites “a” and “b” (holes) on the Fg molecule with similar binding free energies of about −34 kJ mol−1. Altogether, these findings confirmed first that GAS possesses anticoagulant activity and that the possible anticoagulation mechanism of GAS mainly involves its interference with the knob‐to‐hole interactions between fibrin molecules, thereby effectively inhibiting the formation of clots and decreasing the risk of thrombosis. The study has also shown the potential usefulness of QCM biosensor technology for the rapid screening of drug–protein interactions.
Visualizing neurons one‐by‐one in vivo: Optical dissection and reconstruction of neural networks with reversible fluorescent proteins
Authors: Aramaki Shinsuke , Hatta Kohei
Published: July 2006

A great many axons and dendrites intermingle to fasciculate, creating synapses as well as glomeruli. During live imaging in particular, it is often impossible to distinguish between individual neurons when they are contiguous spatially and labeled in the same fluorescent color. In an attempt to solve this problem, we have taken advantage of Dronpa, a green fluorescent protein whose fluorescence can be erased with strong blue light, and reversibly highlighted with violet or ultraviolet light. We first visualized a neural network with fluorescent Dronpa using the Gal4‐UAS system. During the time‐lapse imaging of axonal navigation, we erased the Dronpa fluorescence entirely; re‐highlighted it in a single neuron anterogradely from the soma or retrogradely from the axon; then repeated this procedure for other single neurons. After collecting images of several individual neurons, we then recombined them in multiple pseudo‐colors to reconstruct the network. We have also successfully re‐highlighted Dronpa using two‐photon excitation microscopy to label individual cells located inside of tissues and were able to demonstrate visualization of a Mauthner neuron extending an axon. These “optical dissection” techniques have the potential to be automated in the future and may provide an effective means to identify gene function in morphogenesis and network formation at the single cell level. Developmental Dynamics, 2006. © 2006 Wiley‐Liss, Inc.
Tamoxifen‐inducible NaV1.8‐CreERT2 recombinase activity in nociceptive neurons of dorsal root ganglia
Authors: Zhao Jing , Nassar Mohammed A. , Gavazzi Isabella , Wood John N.
Published: July 2006

To explore the function of genes expressed in adult mouse nociceptive neurons, we generated heterozygous knock‐in mice expressing the tamoxifen‐inducible Cre recombinase construct CreERT2 downstream of the NaV1.8 promoter. CreERT2 encodes a Cre recombinase (Cre) fused to a mutant estrogen ligand‐binding domain (ERT2) that requires the presence of tamoxifen for activity. We have previously shown that heterozygous NaV1.8‐Cre mice will delete loxP flanked genes specifically in nociceptive sensory neurons from embryonic day 14. We therefore used the same strategy of homologous recombination and mouse generation, substituting the Cre cassette with CreERT2. No functional Cre recombinase activity was found in CreERT2 mice crossed with reporter mice in the absence of tamoxifen. We found that, as with NaV1.8‐Cre mice, functional Cre recombinase was present in nociceptive sensory neurons after tamoxifen induction in vivo. However, the percentage of dorsal root ganglion (DRG) neurons expressing functional Cre activity was much reduced (<10% of the number found in the NaV1.8‐Cre mouse). We also examined Cre recombinase activity in sensory neurons in culture. After treatment with 1 μM tamoxifen for 48 h, 15% of DRG neurons showed Cre activity. NaV1.8‐CreERT2 animals may thus be useful for single cell studies of the functional consequences of gene ablation in culture, but are unlikely to be useful for behavioral studies. genesis 44:364–371, 2006. © 2006 Wiley‐Liss, Inc.
Rx‐Cre, a tool for inactivation of gene expression in the developing retina
Authors: Swindell Eric C. , Bailey Travis J. , Loosli Felix , Liu Chaomei , Amaya‐Manzanares Felipe , Mahon Kathleen A. , Wittbrodt Joachim , Jamrich Milan
Published: July 2006

Rx is a homeobox‐containing gene that is critical for vertebrate eye development. Its expression domain delineates a field of cells from which the retina and the ventral hypothalamus develop. The 5′ upstream regulatory sequences of the medaka fish Rx gene are functionally conserved during evolution to a degree that they direct gene expression into the Rx‐expressing field of cells in mice. Using these sequences, we made a Cre line that can be used for inactivation of gene expression in the developing retina. genesis 44:361–363, 2006. Published 2006 Wiley‐Liss, Inc.