Functional architecture and spike timing properties of corticofugal projections from rat ventral temporal cortex

Sensory association and parahippocampal cortex in the ventral temporal lobe plays an important role in sensory object recognition and control of top-down attention. Although layer V neurons located in high-order cortical structures project to multiple cortical and subcortical regions, the architecture and functional organization of this large axonal network are poorly understood. Using a large in vitro slice preparation, we examined the functional organization and spike timing properties of the descending layer V axonal network. We found that most, if not all, layer V neurons in this region can form multiple axonal pathways that project to many brain structures, both proximal and remote. The conduction velocities of different axonal pathways are highly diverse and can vary up to more than threefold. Nevertheless for those axonal projections on the ipsilateral side, the speeds of axonal conduction appear to be tuned to their length. As such, spike delivery becomes nearly isochronic along these pathways regardless of projection distance. In contrast, axons projecting to the contralateral hemisphere are significantly slower and do not participate in this lateralized isochronicity. These structural and functional features of layer V network from the ventral temporal lobe may play an important role in top-down control of sensory cue processing and attention.

Comparison of several hetero-nuclear dipolar recoupling NMR methods to be used in MAS HMQC/HSQC

We compare several hetero-nuclear dipolar recoupling sequences available for HMQC or HSQC experiments applied to spin-1/2 and quadrupolar nuclei. These sequences, which are applied to a single channel, are based either on the rotary resonance recoupling (R3) irradiation, or on two continuous rotor-synchronized modulations (SFAM1 and SFAM2), or on four symmetry-based sequences (R2(1)1,SR4(1)2,R12(3)5,R20(5)9), or on the REDOR scheme. We analyze systems exhibiting purely hetero-nuclear dipolar interactions as well as systems where homo-nuclear dipolar interactions need to be canceled. A special attention is given to the behavior of these sequences at very fast MAS. It is shown that R3 methods behave poorly due to the narrowness of their rf-matching curves, and that the best methods are SR4(1)2 and SFAM (SFAM1 or SFAM2 if homo-nuclear interactions are not negligible). REDOR can also recouple efficiently hetero-nuclear dipolar interactions, provided the sequence is sent on the non-observed channel and homo-nuclear dipolar interactions are negligible. We anticipate that at ultra-fast spinning speed, SFAM1 and SFAM2 will be the most efficient methods.

Through-space MP-CPMAS experiments between spin-1/2 and half-integer quadrupolar nuclei in solid-state NMR

We present a new CPMAS method that allows the acquisition of through-space 2D HETCOR spectra between spin-1/2 nuclei and half-integer quadrupolar nuclei in the solid state. It uses rotor-synchronized selective pulses on the quadrupolar nucleus and continuous-wave RF irradiation on the spin-1/2 nucleus to create hetero-nuclear dipolar coherences. The method is more robust, more efficient, and easier to set up than the standard CPMAS transfer.

Prediction of synergistic transcription factors by function conservation

A new strategy is proposed for identifying synergistic transcription factors by function conservation, leading to the identification of 51 homotypic transcription-factor combinations.

Background

Previous methods employed for the identification of synergistic transcription factors (TFs) are based on either TF enrichment from co-regulated genes or phylogenetic footprinting. Despite the success of these methods, both have limitations.

Results

We propose a new strategy to identify synergistic TFs by function conservation. Rather than aligning the regulatory sequences from orthologous genes and then identifying conserved TF binding sites (TFBSs) in the alignment, we developed computational approaches to implement the novel strategy. These methods include combinatorial TFBS enrichment utilizing distance constraints followed by enrichment of overlapping orthologous genes from human and mouse, whose regulatory sequences contain the enriched TFBS combinations. Subsequently, integration of function conservation from both TFBS and overlapping orthologous genes was achieved by correlation analyses. These techniques have been used for genome-wide promoter analyses, which have led to the identification of 51 homotypic TF combinations; the validity of these approaches has been exemplified by both known TF-TF interactions and function coherence analyses. We further provide computational evidence that our novel methods were able to identify synergistic TFs to a much greater extent than phylogenetic footprinting.

Conclusion

Function conservation based on the concordance of combinatorial TFBS enrichment along with enrichment of overlapping orthologous genes has been proven to be a successful means for the identification of synergistic TFs. This approach avoids the limitations of phylogenetic footprinting as it does not depend upon sequence alignment. It utilizes existing gene annotation data, such as those available in GO, thus providing an alternative method for functional TF discovery and annotation.

The early and initiation processes of radiation-induced bystander effects involved in the induction of DNA double strand breaks in non-irradiated cultures

The initiation and the early process of bystander response induced by low dose alpha-particle irradiation are very important for understanding the mechanisms underlying the bystander response. Using a 1 cGy alpha-particle to irradiate 50% of the area of a rectangular mylar dish, time-dependent DNA double strand breaks (DSBs) were induced shortly after irradiation in AG1522 cells, located either in the irradiated area or in the non-irradiated bystander area, reaching a maximum 30 min post irradiation. Medium transfer experiments showed that the conditioned medium harvested from the irradiated culture induced excessive DNA DSBs in the medium recipient cells, and the DSB-inducing ability of the medium showed was time-dependent. The medium transfer results indicated that the soluble bystander signalling molecule(s) had been generated very soon (probably less than 2.5 min) after irradiation and exist continuously to 30 min although the production of signalling molecule(s) decreased after 10 min post irradiation. Pre-treatment with dimethyl sulphoxide (DMSO) eliminated the DNA DSB-inducing ability of the conditioned medium, as well as the formation of excessive DNA DSBs in both irradiated and non-irradiated bystander areas, indicating that reactive oxygen/nitrogen species etc. might be involved in these processes.

Through-space R3-HETCOR experiments between spin-1/2 and half-integer quadrupolar nuclei in solid-state NMR

We present several new methods that allow to obtain through-space 2D HETCOR spectra between spin-1/2 and half-integer quadrupolar nuclei in the solid state. These methods use the rotary-resonance concept to create hetero-nuclear coherences through the dipolar interaction instead of scalar coupling into the HMQC and refocused INEPT experiments for spin n/2 (n>1). In opposite to those based on the cross-polarization transfer to quadrupolar nuclei, the methods are very robust and easy to set-up.

Altered expression of genes involved in regulation of vitamin A metabolism, solute transportation, and cytoskeletal function in the androgen-insensitive tfm mouse testis

Androgens are essential for the development and maintenance of spermatogenesis, but the underlying mechanisms of androgen action in the testis remain unclear. To help clarify these mechanisms, gene expression was measured in testes of pubertal (20 d old), androgen-insensitive, testicular feminized (Tfm) mice and in normal controls. Using microarrays (Affymetrix chips 430A and 430B), initial data identified a large number of genes down-regulated in the Tfm testis (>4700). These genes were largely of germ cell origin, reflecting the arrest of spermatogenesis that is apparent in the 20-d-old Tfm testis. Subsequent screening in vitro and in silico of this gene set identified 20 genes of a somatic tubular origin that were significantly down-regulated in the Tfm testis and six genes that were significantly up-regulated. Altered expression of these genes was confirmed by real-time PCR, and genes down-regulated in the Tfm testis were shown to be up-regulated in testes of hypogonadal (hpg) mice treated with androgen. In a developmental study using real-time PCR most of the regulated genes showed normal expression during fetal and neonatal development and deviated from control only between 10 and 20 d. In all cases, expression was also reduced in the adult, although interpretation is more complex because of the inherent cryptorchidism in the adult Tfm mouse. Of the total number of somatic genes showing differential expression in the Tfm testis, 50% were associated with three separate groups of genes involved in regulation of vitamin A metabolism, solute transportation, and cytoskeletal function. Thus, effects of androgens on tubular function and spermatogenesis may be mediated in part through regulation of the tubular environment and control of retinoic acid concentrations.

Identification of mutations of zona pellucida glycoprotein (ZP3) and its association with pig reproductive traits

Reproduction is a complex trait, controlled by genetic and environmental factors. Genetic improvement of this trait is important for animal breeders to improve the animal's production efficiency. Apart from genetic factors, animal production can be affected by environmental factors, i.e. the nursing ability of the sow, which is in turn affected directly by effective teat number (teats producing milk normally, TN) and number of piglets born alive (NBA). The objective of this study was to find new mutations, such as single nucleotide polymorphisms (SNPs) from the Zona Pellucida glycoprotein gene (ZP3) using Single Strand Chain Polymorphism (SSCP) and nucleotide sequencing and to investigate association between genetic variations and sow reproductive traits. We identified 13 new SNPs from exon 1, two new SNPs from intron 2, one SNP from intron 6 and a 18 bp (GCACGTGGTCCTCCTGG)-deletion/insertion from intron 2 of the ZP3 gene. Five out of these mutations were selected to genotype in five different breeds (Small Meishan, Qingping, Duroc, Landrace and Large White) and association with reproductive traits in European breeds (Duroc, Landrace and Large White). The sows with genotype AA had more 1.11 piglets NBA than of the sows with genotype AB (p < 0.05) in the 18 bp deletion/insertion of intron 2, while non-significant associations between the other mutations and reproductive traits (NBA and TN) were found.

Peroral transgastric endoscopic primary repair of a ventral hernia in a porcine model

BACKGROUND AND STUDY AIMS

Multiple studies have demonstrated the feasibility of peroral transgastric endoscopic procedures in animal models. The aim of the study was to evaluate the feasibility of a peroral transgastric endoscopic approach to repair abdominal wall hernias.

PATIENTS AND METHODS

We performed acute experiments under general anesthesia with endotracheal intubation using 50-kg pigs. Following peroral intubation an incision of the gastric wall was made and the endoscope was advanced into the peritoneal cavity. An internal anterior abdominal wall incision was performed with a needle knife to create an animal model of a ventral hernia. After hernia creation an endoscopic suturing device was used for primary repair of the hernia. After completion of the hernia repair the endoscope was withdrawn into the stomach and the gastric wall incision was closed with endoscopic clips. Then the animals were killed for necropsy.

RESULTS

Two acute experiments were performed. Incision of the gastric wall was easily achieved with a needle knife and a pull-type sphincterotome. A large (3 x 2 cm) defect of the abdominal wall (ventral hernia model) was closed with five or six sutures using the endoscopic suturing device. Postmortem examination revealed complete closure of the hernia without any complications.

CONCLUSIONS

Transgastric endoscopic primary repair of ventral hernias in a porcine model is feasible and may be technically simpler than laparoscopic surgery.

An essential role for CCAAT/enhancer binding protein beta in bleomycin-induced pulmonary fibrosis

Pulmonary fibrosis is characterized by inflammation, genesis of myofibroblasts, and abnormal tissue repair. Despite extensive research, its pathogenesis remains incompletely understood. Previously, the transcription factor CCAAT/enhancer binding protein beta (C/EBPbeta) was found to be a key regulator of myofibroblast differentiation in vitro, and to be involved in the acute phase and inflammatory responses. In an attempt to test the role of C/EBPbeta in the development of pulmonary fibrosis, experiments using C/EBPbeta null mice and their wild-type littermates were conducted. Our findings indicated that, compared to wild-type mice, animals deficient in C/EBPbeta showed significantly reduced fibrotic lesions and collagen deposition in the lung upon endotracheal injection of bleomycin. Further studies on the mechanisms by which C/EBPbeta regulates fibrosis indicated that knockout of C/EBPbeta attenuates inflammatory cytokine expression in bleomycin-treated mice. The reduced alpha-smooth muscle actin gene expression in either isolated lung fibroblasts or lung tissue from bleomycin or saline-treated C/EBPbeta deficient mice suggests that C/EBPbeta regulates myofibroblast differentiation during fibrosis. Consistent with this finding, cells from C/EBPbeta deficient mice exhibited higher proliferative rates than those from wild-type mice. These data suggest that C/EBPbeta plays an essential role in pulmonary fibrosis and that this role appears to be multifactorial with respect to cytokine expression, cell differentiation, and proliferation.

Proton spin structure in the resonance region

We have examined the spin structure of the proton in the region of the nucleon resonances (1.085 GeV<W<1.910 GeV) at an average four momentum transfer of Q2=1.3 GeV2. Using the Jefferson Lab polarized electron beam, a spectrometer, and a polarized solid target, we measured the asymmetries A|| and A(perpendicular) to high precision, and extracted the asymmetries A1 and A2, and the spin structure functions g1 and g2. We found a notably nonzero A(perpendicular), significant contributions from higher-twist effects, and only weak support for polarized quark-hadron duality.

Neuropilin-1 promotes human glioma progression through potentiating the activity of the HGF/SF autocrine pathway

Neuropilin-1 (NRP1) functions as a coreceptor through interaction with plexin A1 or vascular endothelial growth factor (VEGF) receptor during neuronal development and angiogenesis. NRP1 potentiates the signaling pathways stimulated by semaphorin 3A and VEGF-A in neuronal and endothelial cells, respectively. In this study, we investigate the role of tumor cell-expressed NRP1 in glioma progression. Analyses of human glioma specimens (WHO grade I-IV tumors) revealed a significant correlation of NRP1 expression with glioma progression. In tumor xenografts, overexpression of NRP1 by U87MG gliomas strongly promoted tumor growth and angiogenesis. Overexpression of NRP1 by U87MG cells stimulated cell survival through the enhancement of autocrine hepatocyte growth factor/scatter factor (HGF/SF)/c-Met signaling. NRP1 not only potentiated the activity of endogenous HGF/SF on glioma cell survival but also enhanced HGF/SF-promoted cell proliferation. Inhibition of HGF/SF, c-Met and NRP1 abrogated NRP1-potentiated autocrine HGF/SF stimulation. Furthermore, increased phosphorylation of c-Met correlated with glioma progression in human glioma biopsies in which NRP1 is upregulated and in U87MG NRP1-overexpressing tumors. Together, these data suggest that tumor cell-expressed NRP1 promotes glioma progression through potentiating the activity of the HGF/SF autocrine c-Met signaling pathway, in addition to enhancing angiogenesis, suggesting a novel mechanism of NRP1 in promoting human glioma progression.

Rapid eye movement sleep deprivation selectively impairs recall of fear extinction in hippocampus-independent tasks in rats

Previous studies have shown that rapid eye movement (REM) sleep deprivation (RSD) exerts a detrimental effect on some memory tasks. However, whether post-learning RSD impairs memory for fear extinction, an important model of inhibitory learning, remains to be elucidated. The present study examined the effects of post-extinction RSD from 0 to 6 h and 6 to 12 h on recall of fear extinction tested 24 h after extinction training. We found that RSD from 0 to 6 h significantly increased freezing when recall of extinction of cued fear was tested in the context in which rats received extinction training whereas RSD from 6 to 12 h had no effect (experiments 1 and 2, two hippocampus-independent memory tasks). RSD at either time point had no effect on freezing when recall of extinction of cued fear was tested in the context different from that in which extinction training occurred (experiment 3, a hippocampus-dependent memory task). Additionally, we observed no effect of RSD at either time point on freezing during recall test for extinction of contextual fear (experiment 4, a hippocampus-dependent memory task). These results suggest that the effects of post-extinction RSD on memory for fear extinction are complex. RSD impairs recall of fear extinction in hippocampus-independent tasks, but does not affect recall of fear extinction in hippocampus-dependent tasks. Our findings extend previous research on the effects of RSD on learning and memory and support the notion that REM sleep is involved in memory process of certain tasks.

A new expression plasmid in Bifidobacterium longum as a delivery system of endostatin for cancer gene therapy

To utilize Bifidobacterium longum (B. longum) as a safe and stable delivery system for endostatin in cancer gene therapy, we constructed pBV22210 vector combining a chloramphenicol-resistance gene (Cm(r)) from pBCSK(+) plasmid, a cryptic plasmid pMB1 from B. longum strain with pBV222. Endostatin was cloned directly downstream of an N terminal His6-tag sequence in the pBV22210, so that the endostatin protein expressed in B. longum could be purified with Ni-binding resin. The results indicated that the plasmid electroporated into B. longum was maintained stably in the absence of selective antibiotics and did not significantly affect biological characteristics of B. longum. In addition, the plasmid in B. longum showed a strong inhibitory effect on the growth of mouse solid liver tumor in vivo. These results suggested that this new plasmid may be a stable vector in B. longum for transporting anti-cancer genes in cancer gene therapy.

Localized modes in open one-dimensional dissipative random systems

We consider, both theoretically and experimentally, the excitation and detection of the localized quasimodes (resonances) in an open dissipative 1D random system. We show that, even though the amplitude of transmission drops dramatically so that it cannot be observed in the presence of small losses, resonances are still clearly exhibited in reflection. Surprisingly, small losses essentially improve conditions for the detection of resonances in reflection as compared with the lossless case. An algorithm is proposed and tested to retrieve sample parameters and resonance characteristics inside the random system exclusively from reflection measurements.

Axonal and somatic filtering of antidromically evoked cortical excitation by simulated deep brain stimulation in rat brain

Antidromic cortical excitation has been implicated as a contributing mechanism for high-frequency deep brain stimulation (DBS). Here, we examined the reliability of antidromic responses of type 2 corticofugal fibres in rat over a stimulation frequency range compatible to the DBS used in humans. We activated antidromically individual layer V neurones by stimulating their two subcortical axonal branches. We found that antidromic cortical excitation is not as reliable as generally assumed. Whereas the fast conducting branches of a type 2 axon in the highly myelinated brainstem region follow high-frequency stimulation, the slower conducting fibres in the poorly myelinated thalamic region function as low-pass filters. These fibres fail to transmit consecutive antidromic spikes at the beginning of high-frequency stimulation, but are able to maintain a steady low-frequency (6-12 Hz) spike output during the stimulation. In addition, antidromic responses evoked from both branches are rarely present in cortical neurones with a more hyperpolarized membrane potential. Our data indicate that axon-mediated antidromic excitation in the cortex is strongly influenced by the myelo-architecture of the stimulation site and the excitability of individual cortical neurones.

Thermal rectifying effect in macroscopic size

We address the problem of the rectifying effect of heat conduction at macroscopic size. A design for a macroscopic thermal rectifier based on the macroscopic thermal conductivity of materials is introduced, and then realizations of the design are shown by numerical simulations and phenomenological estimations.

Dimensional crossover of heat conduction in low dimensions

The dimensional crossover phenomena of heat conduction is studied by a two-dimensional (2D) Fermi-Pasta-Ulam lattice. The 2D divergence law of the thermal conductivity is confirmed by the simulations results. The divergence law of the thermal conductivity will change from the 2D class to 1D class as delta=N{y}N{x} decreases, here N{y} is the size in transverse direction and Nx in longitude direction. The simulation's results suggest that the dimensional crossover happens in delta{*}-->0 as N{x}-->infinity .

Asymmetric heat conduction through a weak link

We study the heat conduction of two nonlinear lattices joined by a weak harmonic link. When the system reaches a steady state, the heat conduction of the system is decided by the tunneling heat flow through the weak link. We present an analytical analysis by the combination of the self-consistent phonon theory and the heat tunneling transport formalism, and then the tunneling heat flow can be obtained. Moreover, the nonequilibrium molecular dynamics simulations are performed and the simulations results are consistent with the analytical predictions.

Electrical Property of Mo-Doped VO2 Nanowire Array Film by Melting−Quenching Sol−Gel Method

Mo-doped VO(2) nanowire array film with good thermochromic properties was prepared by melting-quenching followed by heat treatment in a vacuum. The formation of the new microstructure is related to the cleavage of the oxide lamella along (001) and (100) plane with large interplanar spacing. Mo doping results in the loss of V(4+)-V(4+) pairs and destabilizes the semiconductor phase and consequently lowers the semiconductor-to-metal transition temperature T(c) from 64 to 42 degrees C. Because of enhancement of the electron concentration due to the presence of Mo donors, the Fermi level shifts toward the conduction band, resulting in the decrease of activation energy E(a), hence, temperature coefficient of resistance.