bluuebunny/crossref_metadata_2025 huggingface dataset:
Oxidized and poorly glycosylated band 3 is selectively phosphorylated by Syk kinase to form large membrane clusters in normal and G6PD-deficient red blood cells
Authors: Pantaleo Antonella , Ferru Emanuela , Giribaldi Giuliana , Mannu Franca , Carta Franco , Matte Alessandro , de Franceschi Lucia , Turrini Franco
Published: October 2008

Oxidative events involving band 3 (Anion Exchanger 1) have been associated with RBC (red blood cell) removal through binding of NAbs (naturally occurring antibodies); however, the underlying mechanism has been only partially characterized. In addition to inducing direct membrane protein oxidative modification, oxidative treatment specifically triggers the phosphorylation of band 3 tyrosine residues. The present study reports that diamide, a thiol group oxidant, induces disulfide cross-linking of poorly glycosylated band 3 and that the oligomerized band 3 fraction is selectively tyrosine phosphorylated both in G6PD (glucose-6-phosphate dehydrogenase)-deficient and control RBCs. This phenomenon is irreversible in G6PD-deficient RBCs, whereas it is temporarily limited in control RBCs. Diamide treatment caused p72 Syk phosphorylation and translocation to the membrane. Diamide also induced p72 Syk co-immunoprecipitation with aggregated band 3. Moreover, following size-exclusion separation of Triton X-100-extracted membrane proteins, Syk was found only in the high-molecular-mass fraction containing oligomerized/phosphorylated band 3. Src family inhibitors efficiently abrogated band 3 tyrosine phosphorylation, band 3 clustering and NAbs binding to the RBC surface, suggesting a causal relationship between these events. Experiments performed with the non-permeant cross-linker BS3 (bis-sulfosuccinimidyl-suberate) showed that band 3 tyrosine phosphorylation enhances its capability to form large aggregates. The results of the present study suggest that selective tyrosine phosphorylation of oxidized band 3 by Syk may play a role in the recruitment of oxidized band 3 in large membrane aggregates that show a high affinity to NAbs, leading to RBC removal from the circulation.
Muscle acylcarnitines during short-term fasting in lean healthy men
Authors: Soeters Maarten R. , Sauerwein Hans P. , Duran Marinus , Wanders Ronald J. , Ackermans Mariëtte T. , Fliers Eric , Houten Sander M. , Serlie Mireille J.
Published: October 2008

The transition from the fed to the fasted resting state is characterized by, among other things, changes in lipid metabolism and peripheral insulin resistance. Acylcarnitines have been suggested to play a role in insulin resistance, as well as other long-chain fatty acid metabolites. Plasma levels of long-chain acylcarnitines increase during fasting, but this is unknown for muscle long-chain acylcarnitines. In the present study we investigated whether muscle long-chain acylcarnitines increase during fasting and we investigated their relationship with glucose/fat oxidation and insulin sensitivity in lean healthy humans. After 14 h and 62 h of fasting, glucose fluxes, substrate oxidation, and plasma and muscle acylcarnitines were measured before and during a hyperinsulinaemic–euglycaemic clamp. Hyperinsulinaemia decreased long-chain muscle acylcarnitines after 14 h of fasting, but not after 62 h of fasting. In both the basal state and during the clamp, glucose oxidation was lower and fatty acid oxidation was higher after 62 h compared with 14 h of fasting. Absolute changes in glucose and fatty acid oxidation in the basal compared with hyperinsulinaemic state were not different. Muscle long-chain acylcarnitines did not correlate with glucose oxidation, fatty acid oxidation or insulin-mediated peripheral glucose uptake. After 62 h of fasting, the suppression of muscle long-chain acylcarnitines by insulin was attenuated compared with 14 h of fasting. Muscle long-chain acylcarnitines do not unconditionally reflect fatty acid oxidation. The higher fatty acid oxidation during hyperinsulinaemia after 62 h compared with 14 h of fasting, although the absolute decrease in fatty acid oxidation was not different, suggests a different set point.
A local contracted treatment of single and double excitations
Authors: Reinhardt P. , Zhang H. , Ma J. , Malrieu J.-P.
Published: October 2008

Starting from localized bond or lone-pair Hartree–Fock molecular orbitals, one may define contracted doubly excited functions for each pair of bond molecular orbitals. These functions are obtained from local single- and double-configuration interaction (CISD) of moderate size. Then one may build a contracted CISD matrix for the whole molecule, spanned by the Hartree–Fock determinant and these contracted doubly excited functions, the number of which is indeed moderate, as scaling at most as the square of the number of bonds. The calculation of the off-diagonal elements of this matrix is straightforward. Its diagonalization provides an upper bound to the lowest CISD eigenvalue. The well-known size-consistency error may be overcome through self-consistent dressings such as coupled-electron pair approximations, and cutoff criteria will lead to linear scaling. Numerical tests on a series of covalent and ionic systems show that the results are very close to that of coupled-cluster calculations. Possible improvements of this already efficient algorithm are suggested.
Plasmon resonances of aluminum nanoparticles and nanorods
Authors: Ekinci Y. , Solak H. H. , Löffler J. F.
Published: October 2008

We report experimental and theoretical analysis of the plasmonic resonances of Al nanoparticles and nanorods. Ordered nanoparticle arrays with well-defined shapes and narrow size distributions are fabricated on quartz substrates over large areas using extreme ultraviolet interference lithography. The structures, which have sizes down to 40 nm, exhibit strong and sharp particle plasmon resonances in the near and deep-UV ranges. A comprehensive theoretical analysis carried out using dipolar approximation and finite-difference time-domain methods shows good overall agreement with measurements while revealing the dependence of the optical response of Al structures on the fabrication conditions. The results demonstrate the suitability of using Al as a plasmonic material in the UV range and the feasibility of extending applications of plasmonics, such as surface-enhanced Raman spectroscopy, down to the deep-UV range.
Progesterone regulation of the endometrial WNT system in the ovine uterus
Authors: Satterfield M. Carey , Song Gwonhwa , Hayashi Kanako , Bazer Fuller W. , Spencer Thomas E.
Published: October 2008

WNT signalling regulates cell proliferation, differentiation, polarity and organisation. The present study investigated the effects of progesterone (P4) on the endometrial WNT system in relation to blastocyst development and growth in sheep. Ewes received daily intramuscular injections of either corn oil (CO) vehicle or 25 mg P4 from 36 h after mating (Day 0) until hysterectomy on Day 9 or 12. Another group received P4 until Day 8 and 75 mg mifepristone (RU486) from Day 8 to Day 12. Early P4 treatment increased blastocyst growth on Days 9 and 12, whereas no blastocysts were recovered from P4 + RU486-treated ewes. Levels of WNT2 mRNA in the stroma and WNT11 and WNT7A mRNAs in the endometrial luminal epithelia (LE) were reduced in P4 + RU486-treated ewes on Day 9, whereas WNT11 mRNA was reduced in the endometria of both P4- and P4 + RU486-treated ewes on Day 12. On Day 12, WNT2 mRNA was increased in the stroma, WNT7A mRNA was increased in the LE and WNT5A mRNA was increased in the LE and stroma of P4 + RU486- compared with P4-treated ewes. DKK1 mRNA was absent in the endometrial stroma of P4 + RU486-treated ewes. Expression of transcription factor 7 like-2 (TCF7L2) was transiently increased in endometrial epithelia of P4-treated ewes on Day 9, but decreased in these ewes on Day 12. MSX1 mRNA was decreased by P4 treatment on Day 9 and levels of both MSX1 and MSX2 mRNA were higher in P4 + RU486-treated ewes on Day 12. Thus, P4 modulates the endometrial WNT system and elicits a transient decline in selected WNT pathways and signalling components, which is hypothesised to alter tight and adherens junctions, thereby stimulating blastocyst growth and development.
Expression and regulation of lanosterol 14α-demethylase in mouse embryo and uterus during the peri-implantation period
Authors: Song Xiaoming , Tai Ping , Yan Jun , Xu Baoshan , Chen Xiufen , Ouyang Hong , Zhang Meijia , Xia Guoliang
Published: October 2008

Lanosterol 14α-demethylase (LDM) is expressed ubiquitously in all mammals and is important in cholesterol biosynthesis. However, whether LDM expression is involved in the interaction between uterus and embryo during implantation remains unknown. In the present study, the expression of LDM was investigated in mouse embryo and uterus during the peri-implantation period using confocal microscopy, immunohistochemistry and western blot methods. Further, regulation of LDM expression was investigated in pseudopregnancy, delayed implantation, artificial decidualisation and ovariectomisation using 17β-oestradiol and progesterone treatment mouse models. The results showed that LDM was selectively expressed in preimplantation embryos and the uterine subluminal stroma surrounding the implanting blastocyst on Day 5 of pregnancy. No corresponding signal was detected in the uterus on Day 5 of pseudopregnancy. Most notably, once delayed implantation was terminated by oestrogen treatment and the embryo implanted, a high level of LDM expression was induced in the subluminal stroma surrounding the implanting blastocyst, whereas no corresponding signal was detected in the delayed implantation uterus. A high level of LDM expression was observed in the uterus decidua on Days 6–8 of pregnancy. Furthermore, LDM expression was induced in the uterine stroma under artificial decidualisation. Oestrogen, but not progesterone, treatment induced a high level of LDM expression in the uterus of ovariectomised mice. These results indicate that LDM is closely related to mouse embryo implantation and can be upregulated by oestrogen.
Expression pattern of zygote arrest 1 (ZAR1), maternal antigen that embryo requires (MATER), growth differentiation factor 9 (GDF9) and bone morphogenetic protein 15 (BMP15) genes in ovine oocytes and in vitro-produced preimplantation embryos
Authors: Bebbere Daniela , Bogliolo Luisa , Ariu Federica , Fois Stefano , Leoni Giovanni Giuseppe , Tore Silvia , Succu Sara , Berlinguer Fiammetta , Naitana Salvatore , Ledda Sergio
Published: October 2008

The expression patterns of four maternal effect genes (MEG), namely zygote arrest 1 (ZAR1), maternal antigen that embryo requires (MATER), growth differentiation factor 9 (GDF9) and bone morphogenetic protein 15 (BMP15), were determined in ovine oocytes and in vitro-produced preimplantation embryos. The existence of ZAR1 and MATER in ovine species has not been reported previously. Reverse transcription–polymerase chain reaction was performed on germinal vesicle and IVM MII oocytes, as well as in in vitro fertilised and cultured two-, four-, eight- and 12/16-cell embryos, morulae and blastocysts. Quantification of gene expression by real-time polymerase chain reaction showed the highest abundance of all transcripts analysed in the immature oocyte. During the following stages of preimplantation development, the mRNAs examined exhibited different patterns of expression, but often significant decreases were observed during maturation and maternal–embryonic transition. The transcription of the four genes did not resume with activation of the genome.
Growth and differentiation factor-9 stimulates activation of goat primordial follicles in vitro and their progression to secondary follicles
Authors: Martins F. S. , Celestino J. J. H. , Saraiva M. V. A. , Matos M. H. T. , Bruno J. B. , Rocha-Junior C. M. C. , Lima-Verde I. B. , Lucci C. M. , Báo S. N. , Figueiredo J. R.
Published: October 2008

The aim of the present study was to investigate the effects of growth and differentiation factor-9 (GDF-9) on the survival and activation of preantral follicles, as well as their subsequent progression to secondary follicles, using goat ovarian cortical culture in vitro. Pieces of ovarian cortex were cultured for 1 and 7 days in minimum essential medium (MEM) with or without different concentrations of GDF-9 (1–200 ng mL–1). On Day 0 and after 1 and 7 days of culture, cortical pieces were fixed for histological and transmission electron microscopy evaluation. Preantral follicles were classified according to their development stage (primordial, intermediate, primary and secondary) and on the basis of morphological features (normal or degenerated). In addition, follicular and oocyte diameters were determined before and after culture. The results showed that, compared with non-cultured cortical tissue (Day 0), the culture of ovarian tissue significantly reduced (P < 0.05) the percentage of normal follicles in all media tested, except for tissue cultured in the presence of 200 ng mL–1 GDF-9. Furthermore, in all media tested, the percentage of primordial follicles was significantly reduced (P < 0.05), with a concomitant increase in the percentage of developing follicles. The highest percentage of secondary follicles was observed after 7 days of culture in MEM plus 200 ng mL–1 GDF-9. At all concentrations of GDF-9 tested, follicular diameter increased significantly after 7 days of culture compared with non-cultured cortical tissue. In conclusion, the results of the present study indicate that 200 ng mL–1 GDF-9 maintains the survival of preantral follicles and promotes activation of primordial follicles. Furthermore, GDF-9 stimulates the transition from primary to secondary follicles, maintaining ultrastructural integrity of the follicles.
Microinjection of mouse phospholipase Cζ complementary RNA into mare oocytes induces long-lasting intracellular calcium oscillations and embryonic development
Authors: Bedford-Guaus Sylvia J. , Yoon Sook-Young , Fissore Rafael A. , Choi Young-Ho , Hinrichs Katrin
Published: October 2008

Methods presently used to activate mare oocytes for assisted reproduction technologies provide low rates of advanced embryonic development. Because phospholipase Cζ (PLCζ) is the postulated sperm-borne factor responsible for oocyte activation at fertilisation, the aim of the present study was to investigate the pattern of [Ca2+]i oscillations and developmental rates achieved by microinjection of three concentrations of mouse PLCζ complementary (c) RNA (1, 0.5 or 0.25 μg μL–1) into mare oocytes. The frequency of [Ca2+]i oscillations was no different (P > 0.05) after injection of 1, 0.5 or 0.25 μg μL–1 PLCζ cRNA (41.1 ± 5.3, 47 ± 4.0 and 55.4 ± 9.0, respectively). However, [Ca2+]i oscillations persisted longest (P < 0.05) for oocytes injected with 0.5 μg μL–1 PLCζ cRNA (570.7 ± 64.2 min). There was no significant difference in cleavage rates after injection of the three concentrations of PLCζ (P > 0.05; range 97–100%), but the proportion of oocytes reaching advanced stages of embryonic development (>64 nuclei) was significantly lower for oocytes injected with 0.25 μg μL–1 PLCζ cRNA (3%) than for those injected with 1 μg μL–1 PLCζ cRNA (15%). Based on these results, microinjection of PLCζ may prove an effective and consistent method for the parthenogenetic activation of mare oocytes for nuclear transfer and provides a physiologically relevant tool with which to study fertilisation-dependent [Ca2+]i signalling in this species.
Effects of age on follicle and hormone dynamics during the oestrous cycle in mares
Authors: Ginther O. J. , Gastal M. O. , Gastal E. L. , Jacob J. C. , Siddiqui M. A. R. , Beg M. A.
Published: October 2008

The effects of age (young: 5–6 years; intermediate: 10–14 years; old: ≥18 years) on follicle and hormone dynamics during an interovulatory interval (IOI; n = 46) and on preovulatory oocytes and concentrations of follicular fluid factors (n = 44) were studied in mares. Old mares were not approaching senescence, as indicated by regular lengths of the IOI (19–27 days) during the period May–October. The IOI was 1 day longer (P < 0.05) in the old group than in the two younger groups and was associated with a slower (P < 0.05) growth rate of the ovulatory follicle. The old group had diminished follicle activity, as indicated by significantly smaller and fewer follicles. Concentrations of FSH did not differ among age groups, except that the maximum concentration was greater (P < 0.05) in the old group. Concentrations of LH were greater (age × day interaction; P < 0.03) in the young group throughout the ovulatory LH surge and may have played a role in a shorter (P < 0.05) interval from maximum diameter of the preovulatory follicle to ovulation. Maximum circulating concentrations of oestradiol during the preovulatory surge were greatest (P < 0.05) in the young group. No effects of age were detected on oocyte morphology. Concentrations of ovarian steroids in preovulatory follicular fluid were not affected by the age of the mares, but concentrations of free insulin-like growth factor-1 were greater (P < 0.05) in the old group. The results indicate the importance of considering the potential confounding effects of age in experimental protocols and for considering age in the development of theriogenology programmes.
Induction of haemorrhagic anovulatory follicles in mares
Authors: Ginther O. J. , Gastal M. O. , Gastal E. L. , Jacob J. C. , Beg M. A.
Published: October 2008

A follicular wave and luteolysis were induced in mares by ablation of follicles ≥6 mm and treatment with prostaglandin F2α (PGF) on Day 10 (where ovulation = Day 0). The incidence of haemorrhagic anovulatory follicles (HAFs) in the induced waves (20%) was greater (P < 0.007) than in preceding spontaneous waves (2%). Hormone and follicle dynamics were compared between induced follicular waves that ended in ovulations (ovulating group; n = 36) v. HAFs (HAF group; n = 9). The day of the first ovulation or the beginning of HAF formation at the end of an induced wave was designated as post-treatment Day 0. The mean 13-day interval from Day 10 (PGF and ablation) to the post-treatment ovulation was normalised into Days 10 to 16, followed by Day –6 to Day 0 relative to the post-treatment ovulation. Concentrations of LH were greater (P < 0.05) in the HAF group than in the ovulating group on Days 10, 11, 12, 14, –3 and –2. The HAF group had greater (P < 0.003) LH concentrations on Day 10 of the preceding oestrous cycle with spontaneous ovulatory waves. The diameter of the largest follicle was less (P < 0.05) in the HAF group on most days between Day 13 and Day –1 and this was attributable to later (P < 0.002) emergence of the future largest follicle at 6 mm in the HAF group (Day 12.4 ± 0.5) than in the ovulating group (Day 11.3 ± 0.1). The results indicate that the high incidence of HAFs after PGF and ablation was associated with later follicle emergence and immediate and continuing greater LH concentration after PGF treatment, apparently augmented by an inherently high pretreatment LH concentration.
Increased proportion of donor primordial germ cells in chimeric gonads by sterilisation of recipient embryos using busulfan sustained-release emulsion in chickens
Authors: Nakamura Yoshiaki , Yamamoto Yasuhiro , Usui Fumitake , Atsumi Yusuke , Ito Yohei , Ono Tamao , Takeda Kumiko , Nirasawa Keijiro , Kagami Hiroshi , Tagami Takahiro
Published: October 2008

The aim of the present study was to improve the efficiency of endogenous primordial germ cell (PGC) depletion and to increase the ratio of donor PGCs in the gonads of recipient chicken embryos. A sustained-release emulsion was prepared by emulsifying equal amounts of Ca2+- and Mg2+-free phosphate-buffered saline containing 10% busulfan solubilised in N,N-dimethylformamide and sesame oil, using a filter. Then, 75 μg per 50 μL busulfan sustained-release emulsion was injected into the yolk. To determine the depletion and repopulation of PGCs in the gonads after 6 days incubation, whole-mount immunostaining was performed. The busulfan sustained-release emulsion significantly reduced the number of endogenous PGCs compared with control (P < 0.05). Moreover, the busulfan sustained-release emulsion significantly depleted endogenous PGCs compared with other previously reported busulfan delivery systems (P < 0.05), but with less variation, suggesting that the sustained-release emulsion delivered a consistent amount of busulfan to the developing chicken embryos. The PGC transfer study showed that the proportion of donor PGCs in the gonads of busulfan sustained-release emulsion-treated embryos after 6 days incubation increased 28-fold compared with control. In conclusion, the results demonstrate that exogenous PGCs are capable of migrating and settling in gonads from which endogenous PGCs have been removed using a busulfan sustained-release emulsion.
Oestradiol-induced spermatogenesis requires a functional androgen receptor
Authors: Lim Patrick , Allan Charles M. , Notini Amanda J. , Axell Anna-Maree , Spaliviero Jennifer , Jimenez Mark , Davey Rachel , McManus Julie , MacLean Helen E. , Zajac Jeffrey D. , Handelsman David J.
Published: October 2008

Spermatogenesis requires androgen but, paradoxically, oestradiol (E2) treatment stimulates spermatogenic development in gonadotrophin- and androgen-deficient hypogonadal (hpg) mice. The mechanisms of E2-induced spermatogenesis were investigated by determining intratesticular E2 levels and testis cell populations in E2-treated hpg male mice, and E2 spermatogenic actions were determined in androgen receptor-knockout (ARKO) mice. Despite increased serum E2 concentrations (150–300 pmol L–1), intratesticular E2 concentrations declined fivefold (P < 0.001) in E2-treated v. untreated hpg male mice. Serum FSH reached 40% of normal and total testicular numbers of known FSH-responsive Sertoli, spermatogonia and meiotic spermatocyte populations were significantly (P < 0.001) elevated 1.7-, 4- and 13-fold, respectively. However, E2 administration also increased androgen-dependent pachytene spermatocytes and post-meiotic spermatids to levels comparable with testosterone-treated hpg testes. Selective investigation of androgen receptor involvement used E2-treated ARKO mice, which were found to exhibit increased (1.6-fold; P < 0.05) intratesticular E2 concentrations and suppression of the elevated serum gonadotrophins, although FSH remained twofold higher than normal. However, testis size and total Sertoli, spermatogonia and spermatocyte numbers were not increased in E2-treated ARKO male mice. Therefore, E2-stimulated murine spermatogenic development occurs with markedly suppressed and not elevated intratesticular E2 levels and displays an absolute requirement for functional androgen receptors. We propose that this paradoxical E2 spermatogenic response is explained by predominantly extratesticular E2 actions, increasing FSH to combine with residual androgen activity in hpg testes to stimulate pre- to post-meiotic development.
Focal adhesions disassemble during early pregnancy in rat uterine epithelial cells
Authors: Kaneko Yui , Lindsay Laura A. , Murphy Christopher R.
Published: October 2008

During early pregnancy in rodents, invasion of the blastocyst into the endometrial decidual cells is accompanied by the removal of uterine epithelial cells around the implantation sites. The present study investigated the distribution and expression of two focal adhesion proteins, namely talin and paxillin, in rat uterine epithelial cells during early pregnancy and their role in the loss of these cells at the time of implantation. A major distributional change of talin and paxillin was demonstrated in uterine epithelial cells during early pregnancy. From a highly concentrated expression along the basal cell surface on Day 1 of pregnancy, talin and paxillin were lost from the basal cell surface at the time of implantation. There was also a corresponding statistically significant decrease in paxillin seen through western blotting analysis. Together, these observations suggest that uterine epithelial cells are less adherent to the underlying basal lamina due to the disassembly of talin and paxillin from focal adhesions, facilitating removal of these cells at the time of implantation. This phenomenon was restricted to the period of receptivity because talin and paxillin reappeared along the basal cell surface soon after implantation.
Activation of P2X7 receptors in glial satellite cells reduces pain through downregulation of P2X3 receptors in nociceptive neurons
Authors: Chen Yong , Zhang Xiaofei , Wang Congying , Li GuangWen , Gu Yanping , Huang Li-Yen Mae
Published: October 2008

Purinergic ionotropic P2X7 receptors (P2X7Rs) are closely associated with excitotoxicity and nociception. Inhibition of P2X7R activation has been considered as a potentially useful strategy to improve recovery from spinal cord injury and reduce inflammatory damage to trauma. The physiological functions of P2X7Rs, however, are poorly understood, even though such information is essential for making the P2X7R an effective therapeutic target. We show here that P2X7Rs in satellite cells of dorsal root ganglia tonically inhibit the expression of P2X3Rs in neurons. Reducing P2X7R expression using siRNA or blocking P2X7R activity by antagonists elicits P2X3R up-regulation, increases the activity of sensory neurons responding to painful stimuli, and evokes abnormal nociceptive behaviors in rats. Thus, contrary to the notion that P2X7R activation is cytotoxic, P2X7Rs in satellite cells play a crucial role in maintaining proper P2X3R expression in dorsal root ganglia. Studying the mechanism underlying the P2X7R–P2X3R control, we demonstrate that activation of P2X7Rs evokes ATP release from satellite cells. ATP in turn stimulates P2Y1 receptors in neurons. P2Y1 receptor activation appears to be necessary and sufficient for the inhibitory control of P2X3R expression. We further determine the roles of the P2X7R–P2Y1–P2X3R inhibitory control under injurious conditions. Activation of the inhibitory control effectively prevents the development of allodynia and increases the potency of systemically administered P2X7R agonists in inflamed rats. Thus, direct blocking P2X7Rs, as proposed before, may not be the best strategy for reducing pain or lessening neuronal degeneration because it also disrupts the protective function of P2X7Rs.
Side-chain recognition and gating in the ribosome exit tunnel
Authors: Petrone Paula M. , Snow Christopher D. , Lucent Del , Pande Vijay S.
Published: October 2008

The ribosome is a large complex catalyst responsible for the synthesis of new proteins, an essential function for life. New proteins emerge from the ribosome through an exit tunnel as nascent polypeptide chains. Recent findings indicate that tunnel interactions with the nascent polypeptide chain might be relevant for the regulation of translation. However, the specific ribosomal structural features that mediate this process are unknown. Performing molecular dynamics simulations, we are studying the interactions between components of the ribosome exit tunnel and different chemical probes (specifically different amino acid side chains or monovalent inorganic ions). Our free-energy maps describe the physicochemical environment of the tunnel, revealing binding crevices and free-energy barriers for single amino acids and ions. Our simulations indicate that transport out of the tunnel could be different for diverse amino acid species. In addition, our results predict a notable protein–RNA interaction between a flexible 23S rRNA tetraloop (gate) and ribosomal protein L39 (latch) that could potentially obstruct the tunnel's exit. By relating our simulation data to earlier biochemical studies, we propose that ribosomal features at the exit of the tunnel can play a role in the regulation of nascent chain exit and ion flux. Moreover, our free-energy maps may provide a context for interpreting sequence-dependent nascent chain phenomenology.
Adaptive antioxidant methionine accumulation in respiratory chain complexes explains the use of a deviant genetic code in mitochondria
Authors: Bender Aline , Hajieva Parvana , Moosmann Bernd
Published: October 2008

Humans and most other animals use 2 different genetic codes to translate their hereditary information: the standard code for nuclear-encoded proteins and a modern variant of this code in mitochondria. Despite the pivotal role of the genetic code for cell biology, the functional significance of the deviant mitochondrial code has remained enigmatic since its first description in 1979. Here, we show that profound and functionally beneficial alterations on the encoded protein level were causative for the AUA codon reassignment from isoleucine to methionine observed in most mitochondrial lineages. We demonstrate that this codon reassignment leads to a massive accumulation of the easily oxidized amino acid methionine in the highly oxidative inner mitochondrial membrane. This apparently paradoxical outcome can yet be smoothly settled if the antioxidant surface chemistry of methionine is taken into account, and we present direct experimental evidence that intramembrane accumulation of methionine exhibits antioxidant and cytoprotective properties in living cells. Our results unveil that methionine is an evolutionarily selected antioxidant building block of respiratory chain complexes. Collective protein alterations can thus constitute the selective advantage behind codon reassignments, which authenticates the “ambiguous decoding” hypothesis of genetic code evolution. Oxidative stress has shaped the mitochondrial genetic code.
The ubiquitin ligase Siah2 regulates tumorigenesis and metastasis by HIF-dependent and -independent pathways
Authors: Qi Jianfei , Nakayama Koh , Gaitonde Supriya , Goydos James S. , Krajewski Stan , Eroshkin Alexey , Bar-Sagi Dafna , Bowtell David , Ronai Ze'ev
Published: October 2008

The ubiquitin ligase Siah2 has been shown to regulate prolyl hydroxylase 3 (PHD3) stability with concomitant effect on HIF-1α availability. Because HIF-1α is implicated in tumorigenesis and metastasis, we used SW1 mouse melanoma cells, which develop primary tumors with a propensity to metastasize, in a syngeneic mouse model to assess a possible role for Siah2 in these processes. Inhibiting Siah2 activity by expressing a peptide designed to outcompete association of Siah2-interacting proteins reduced metastasis through HIF-1α without affecting tumorigenesis. Conversely, inhibiting Siah2 activity by means of a dominant-negative Siah2 RING mutant primarily reduced tumorigenesis through the action of Sprouty 2, a negative regulator of Ras signaling. Consistent with our findings, reduced expression of PHD3 and Sprouty2 was observed in more advanced stages of melanoma tumors. Using complementary approaches, our data establish the role of Siah2 in tumorigenesis and metastasis by HIF-dependent and -independent mechanisms.
Small-scale copy number variation and large-scale changes in gene expression
Authors: Mileyko Yuriy , Joh Richard I. , Weitz Joshua S.
Published: October 2008

The expression dynamics of interacting genes depends, in part, on the structure of regulatory networks. Genetic regulatory networks include an overrepresentation of subgraphs commonly known as network motifs. In this article, we demonstrate that gene copy number is an omnipresent parameter that can dramatically modify the dynamical function of network motifs. We consider positive feedback, bistable feedback, and toggle switch motifs and show that variation in gene copy number, on the order of a single or few copies, can lead to multiple orders of magnitude change in gene expression and, in some cases, switches in deterministic control. Further, small changes in gene copy number for a 3-gene motif with successive inhibition (the “repressilator”) can lead to a qualitative switch in system behavior among oscillatory and equilibrium dynamics. In all cases, the qualitative change in expression is due to the nonlinear nature of transcriptional feedback in which duplicated motifs interact via common pools of transcription factors. We are able to implicitly determine the critical values of copy number which lead to qualitative shifts in system behavior. In some cases, we are able to solve for the sufficient condition for the existence of a bifurcation in terms of kinetic rates of transcription, translation, binding, and degradation. We discuss the relevance of our findings to ongoing efforts to link copy number variation with cell fate determination by viruses, dynamics of synthetic gene circuits, and constraints on evolutionary adaptation.
Electric field-induced direct delivery of proteins by a nanofountain probe
Authors: Loh Owen Y. , Ho Andrea M. , Rim Jee E. , Kohli Punit , Patankar Neelesh A. , Espinosa Horacio D.
Published: October 2008

We report nanofabrication of protein dot and line patterns using a nanofountain atomic force microscopy probe (NFP). Biomolecules are continuously fed in solution through an integrated microfluidic system, and deposited directly onto a substrate. Deposition is controlled by application of an electric potential of appropriate sign and magnitude between the probe reservoir and substrate. Submicron dot and line molecular patterns were generated with resolution that depended on the magnitude of the applied voltage, dwell time, and writing speed. By using an energetic argument and a Kelvin condensation model, the quasi-equilibrium liquid–air interface at the probe tip was determined. The analysis revealed the origin of the need for electric fields in achieving protein transport to the substrate and confirmed experimental observations suggesting that pattern resolution is controlled by tip sharpness and not overall probe aperture. As such, the NFP combines the high-resolution of dip-pen nanolithography with the efficient continuous liquid feeding of micropipettes while allowing scalability to 1- and 2D probe arrays for high throughput.
Genes involved in pre-mRNA 3′-end formation and transcription termination revealed by a
lin-15
operon Muv suppressor screen
Authors: Cui Mingxue , Allen Mary Ann , Larsen Alison , MacMorris Margaret , Han Min , Blumenthal Tom
Published: October 2008

RNA polymerase II (Pol II) transcription termination involves two linked processes: mRNA 3′-end formation and release of Pol II from DNA. Signals for 3′ processing are recognized by a protein complex that includes cleavage polyadenylation specificity factor (CPSF) and cleavage stimulation factor (CstF). Here we identify suppressors encoding proteins that play roles in processes at the 3′ ends of genes by exploiting a mutation in which the 3′ end of another gene is transposed into the first gene of the
Caenorhabditis elegans lin-15
operon. As expected, genes encoding CPSF and CstF were identified in the screen. We also report three suppressors encoding proteins containing a domain that interacts with the C-terminal domain of Pol II (CID). We show that two of the CID proteins are needed for efficient 3′ cleavage and thus may connect transcription termination with RNA cleavage. Furthermore, our results implicate a serine/arginine-rich (SR) protein, SRp20, in events following 3′-end cleavage, leading to termination of transcription.
Transport of LDL-derived cholesterol from the NPC1 compartment to the ER involves the trans-Golgi network and the SNARE protein complex
Authors: Urano Yasuomi , Watanabe Hiroshi , Murphy Stephanie R. , Shibuya Yohei , Geng Yong , Peden Andrew A. , Chang Catherine C. Y. , Chang Ta Yuan
Published: October 2008

Mammalian cells acquire cholesterol mainly from LDL. LDL enter the endosomes, allowing cholesteryl esters to be hydrolyzed by acid lipase. The hydrolyzed cholesterol (LDL-CHOL) enters the Niemann–Pick type C1 (NPC1)-containing endosomal compartment en route to various destinations. Whether the Golgi is involved in LDL-CHOL transport downstream of the NPC1 compartment has not been demonstrated. Using subcellular fractionation and immunoadsorption to enrich for specific membrane fractions, here we show that, when parental Chinese hamster ovary (CHO) cells are briefly exposed to
3
H-cholesteryl linoleate (CL) labeled-LDL, newly liberated
3
H-LDL-CHOL appears in membranes rich in trans-Golgi network (TGN) long before it becomes available for re-esterification at the endoplasmic reticulum (ER) or for efflux at the plasma membrane. In mutant cells lacking NPC1, the appearance of newly liberated
3
H-LDL-CHOL in the TGN-rich fractions is much reduced. We next report a reconstituted transport system that recapitulates the transport of LDL-CHOL to the TGN and to the ER. The transport system requires ATP and cytosolic factors and depends on functionality of NPC1. We demonstrate that knockdown by RNAi of 3 TGN-specific SNAREs (VAMP4, syntaxin 6, and syntaxin 16) reduces ≥50% of the LDL-CHOL transport in intact cells and in vitro. These results show that vesicular trafficking is involved in transporting a significant portion of LDL-CHOL from the NPC1-containing endosomal compartment to the TGN before its arrival at the ER.
How the thymus designs antigen-specific and self-tolerant T cell receptor sequences
Authors: Košmrlj Andrej , Jha Abhishek K. , Huseby Eric S. , Kardar Mehran , Chakraborty Arup K.
Published: October 2008

T lymphocytes (T cells) orchestrate adaptive immune responses that clear pathogens from infected hosts. T cells recognize short peptides (p) derived from antigenic proteins bound to protein products of the MHC genes. Recognition occurs when T cell receptor (TCR) proteins expressed on T cells bind sufficiently strongly to antigen-derived pMHC complexes on the surface of antigen-presenting cells. A diverse repertoire of self-pMHC-tolerant TCR sequences is shaped during development of T cells in the thymus by processes called positive and negative selection. Combining computational models and analysis of experimental data, we parsed the contributions of positive and negative selection to the design of TCR sequences that recognize antigenic peptides with specificity, yet also exhibit cross-reactivity. A dominant role for negative selection in mediating antigen specificity of mature T cells and a molecular mechanism for TCR recognition of antigen are described.
Atomic detail of chemical transformation at the transition state of an enzymatic reaction
Authors: Saen-oon Suwipa , Quaytman-Machleder Sara , Schramm Vern L. , Schwartz Steven D.
Published: October 2008

Transition path sampling (TPS) has been applied to the chemical step of human purine nucleoside phosphorylase (PNP). The transition path ensemble provides insight into the detailed mechanistic dynamics and atomic motion involved in transition state passage. The reaction mechanism involves early loss of the ribosidic bond to form a transition state with substantial ribooxacarbenium ion character, followed by dynamic motion from the enzyme and a conformational change in the ribosyl group leading to migration of the anomeric carbon toward phosphate, to form the product ribose 1-phosphate. Calculations of the commitment probability along reactive paths demonstrated the presence of a broad energy barrier at the transition state. TPS identified (
i
) compression of the O4′···O5′ vibrational motion, (
ii
) optimized leaving group interactions, and (
iii
) activation of the phosphate nucleophile as the reaction proceeds through the transition state region. Dynamic motions on the femtosecond timescale provide the simultaneous optimization of these effects and coincide with transition state formation.
Human DNA polymerase η activity and translocation is regulated by phosphorylation
Authors: Chen Yih-wen , Cleaver James E. , Hatahet Zafer , Honkanen Richard E. , Chang Jang-Yang , Yen Yun , Chou Kai-ming
Published: October 2008

Human DNA polymerase η (pol η) can replicate across UV-induced pyrimidine dimers, and defects in the gene encoding pol η result in a syndrome called xeroderma pigmentosum variant (XP-V). XP-V patients are prone to the development of cancer in sun-exposed areas, and cells derived from XP-V patients demonstrate increased sensitivity to UV radiation and a higher mutation rate compared with wild-type cells. pol η has been shown to replicate across a wide spectrum of DNA lesions introduced by environmental or chemotherapeutic agents, or during nucleotide starvation, suggesting that the biological roles for pol η are not limited to repair of UV-damaged DNA. The high error rate of pol η requires that its intracellular activity be tightly regulated. Here, we show that the phosphorylation of pol η increased after UV irradiation, and that treatment with caffeine, siRNA against ATR, or an inhibitor of PKC (calphostin C), reduced the accumulation of pol η at stalled replication forks after UV irradiation or treatment with cisplatin and gemcitabine. Site-specific mutagenesis (S587A and T617A) of pol η at two putative PKC phosphorylation sites located in the protein–protein interaction domain prevented nuclear foci formation induced by UV irradiation or treatment with gemcitabine/cisplatin. In addition, XP-V cell lines stably expressing either the S587A or T617A mutant form of pol η were more sensitive to UV radiation and gemcitabine/cisplatin than control cells expressing wild-type pol η. These results suggest that phosphorylation is one mechanism by which the cellular activity of pol η is regulated.
FADD and caspase-8 control the outcome of autophagic signaling in proliferating T cells
Authors: Bell Bryan D. , Leverrier Sabrina , Weist Brian M. , Newton Ryan H. , Arechiga Adrian F. , Luhrs Keith A. , Morrissette Naomi S. , Walsh Craig M.
Published: October 2008

Fas-associated death domain protein (FADD) and caspase-8 (casp8) are vital intermediaries in apoptotic signaling induced by tumor necrosis factor family ligands. Paradoxically, lymphocytes lacking FADD or casp8 fail to undergo normal clonal expansion following antigen receptor cross-linking and succumb to caspase-independent cell death upon activation. Here we show that T cells lacking FADD or casp8 activity are subject to hyperactive autophagic signaling and subvert a cellular survival mechanism into a potent death process. T cell autophagy, enhanced by mitogenic signaling, recruits casp8 through interaction with FADD:Atg5-Atg12 complexes. Inhibition of autophagic signaling with 3-methyladenine, dominant-negative Vps34, or Atg7 shRNA rescued T cells expressing a dominant-negative FADD protein. The necroptosis inhibitor Nec-1, which blocks receptor interacting protein kinase 1 (RIP kinase 1), also completely rescued T cells lacking FADD or casp8 activity. Thus, while autophagy is necessary for rapid T cell proliferation, our findings suggest that FADD and casp8 form a feedback loop to limit autophagy and prevent this salvage pathway from inducing RIPK1-dependent necroptotic cell death. Thus, linkage of FADD and casp8 to autophagic signaling intermediates is essential for rapid T cell clonal expansion and may normally serve to promote caspase-dependent apoptosis under hyperautophagic conditions, thereby averting necrosis and inflammation in vivo.
Procedure for recording the simultaneous activity of single neurons distributed across cortical areas during sensory discrimination
Authors: Hernández Adrián , Nácher Verónica , Luna Rogelio , Alvarez Manuel , Zainos Antonio , Cordero Silvia , Camarillo Liliana , Vázquez Yuriria , Lemus Luis , Romo Ranulfo
Published: October 2008

We report a procedure for recording the simultaneous activity of single neurons distributed across five cortical areas in behaving monkeys. The procedure consists of a commercially available microdrive adapted to a commercially available neural data collection system. The critical advantage of this procedure is that, in each cortical area, a configuration of seven microelectrodes spaced 250–500 μm can be inserted transdurally and each can be moved independently in the
z
axis. For each microelectrode, the data collection system can record the activity of up to five neurons together with the local field potential (LFP). With this procedure, we normally monitor the simultaneous activity of 70–100 neurons while trained monkeys discriminate the difference in frequency between two vibrotactile stimuli. Approximately 20–60 of these neurons have response properties previously reported in this task. The neuronal recordings show good signal-to-noise ratio, are remarkably stable along a 1-day session, and allow testing several protocols. Microelectrodes are removed from the brain after a 1-day recording session, but are reinserted again the next day by using the same or different x-y microelectrode array configurations. The fact that microelectrodes can be moved in the
z
axis during the recording session and that the x-y configuration can be changed from day to day maximizes the probability of studying simultaneous interactions, both local and across distant cortical areas, between neurons associated with the different components of this task.
Prolonged signaling at the parathyroid hormone receptor by peptide ligands targeted to a specific receptor conformation
Authors: Okazaki Makoto , Ferrandon Sebastien , Vilardaga Jean-Pierre , Bouxsein Mary L. , Potts John T. , Gardella Thomas J.
Published: October 2008

The parathyroid hormone receptor (PTHR) is a class B G protein-coupled receptor that plays critical roles in bone and mineral ion metabolism. Ligand binding to the PTHR involves interactions to both the amino-terminal extracellular (N) domain, and transmembrane/extracellular loop, or juxtamembrane (J) regions of the receptor. Recently, we found that PTH(1–34), but not PTH-related protein, PTHrP(1–36), or M-PTH(1–14) (M = Ala/Aib
1
,Aib
3
,Gln
10
,Har
11
,Ala
12
,Trp
14
,Arg
19
), binds to the PTHR in a largely GTPγS-resistant fashion, suggesting selective binding to a novel, high-affinity conformation (R
0
), distinct from the GTPγS-sensitive conformation (RG). We examined the effects
in vitro
and
in vivo
of introducing the M substitutions, which enhance interaction to the J domain, into PTH analogs extended C-terminally to incorporate residues involved in the N domain interaction. As compared with PTH(1–34), M-PTH(1–28) and M-PTH(1–34) bound to R
0
with higher affinity, produced more sustained cAMP responses in cells, formed more stable complexes with the PTHR in FRET and subcellular localization assays, and induced more prolonged calcemic and phosphate responses in mice. Moreover, after 2 weeks of daily injection in mice, M-PTH(1–34) induced larger increases in trabecular bone volume and greater increases in cortical bone turnover, than did PTH(1–34). Thus, the putative R
0
PTHR conformation can form highly stable complexes with certain PTH ligand analogs and thereby mediate surprisingly prolonged signaling responses in bone and/or kidney PTH target cells. Controlling, via ligand analog design, the selectivity with which a PTH ligand binds to R
0
, versus RG, may be a strategy for optimizing signaling duration time, and hence therapeutic efficacy, of PTHR agonist ligands.
A bacterial control circuit integrates polar localization and proteolysis of key regulatory proteins with a phospho-signaling cascade
Authors: Iniesta Antonio A. , Shapiro Lucy
Published: October 2008

Dynamic protein localization is an integral component of the regulatory circuit that drives the
Caulobacter
cell cycle. The ClpXP protease is localized to the
Caulobacter
cell pole, where it catalyzes the degradation of the CtrA master regulator at specific times in the cell cycle. Clearance of active CtrA at the G1/S transition allows the initiation of DNA replication and cell-cycle progression. The polar localization of ClpXP is dependent on the polar positioning of the CpdR single-domain response regulator. Only the unphosphorylated form of CpdR localizes and activates ClpXP. We demonstrate that another single domain response regulator, DivK, promotes the polar accumulation of unphosphorylated CpdR and that CpdR is subsequently degraded at the cell pole by the localized ClpXP protease. Thus, CpdR function is regulated by a feedback loop that incorporates its differential phosphorylation, the transient polar localization and activity of the ClpXP protease, and the clearance of the CpdR by polar ClpXP that, in turn, releases ClpXP from the pole relieving the degradation of CtrA. CtrA∼P then accumulates and activates the transcription of
cpdR
, completing the regulatory loop, establishing an integrated network that controls a robust cell-cycle transition.