Integrated micro-endoscopy system for simultaneous fluorescence and optical-resolution photoacoustic imaging

We present a new integrated micro-endoscopy system combining label-free, fiber-based, real-time C-scan optical-resolution photoacoustic microscopy (F-OR-PAM) and a high-resolution fluorescence micro-endoscopy system for visualizing fluorescently labeled cellular components and optically absorbing microvasculature simultaneously. With a diode-pumped 532-nm fiber laser, the F-OR-PAM sub-system is able to reach a resolution of ∼7  μm. The fluorescence subsystem, which does not require any mechanical scanning, consists of a 447.5-nm-centered diode laser as the light source, an objective lens, and a CCD camera. Proflavine is used as the fluorescent contrast agent by topical application. The scanning laser and the diode laser light source share the same light path within an optical fiber bundle containing 30,000 individual single-mode fibers. The absorption of proflavine at 532 nm is low, which mitigates absorption bleaching of the contrast agent by the photoacoustic excitation source. We demonstrate imaging in live murine models. The system is able to provide cellular morphology with cellular resolution co-registered with the structural information given by F-OR-PAM. Therefore, the system has the potential to serve as a virtual biopsy technique, helping visualize angiogenesis and the effects of anti-cancer drugs on both cells and the microcirculation, as well as aid in the study of other diseases.

Equilibrium geometries, stabilities, and electronic properties of the cationic Au n Be + (n = 1-8) clusters: comparison with pure gold clusters

Ab initio method based on density functional theory at PW91PW91 level has been applied in studying the geometrical structures, relative stabilities, and electronic properties of small bimetallic Au(n)Be(+) (n = 1-8) cluster cations. The geometrical optimizations indicate that a transition point from preferentially planar (two-dimensional) to three-dimensional (3D) structures occurs at n = 6. The relative stabilities of Au(n)Be(+) clusters for the ground-state structures are analyzed based on the averaged binding energies, fragmentation energies, and second-order difference of energies. The calculated results reveal that the AuBe(+) and Au(5)Be(+) clusters possess higher relative stability for small size Au(n)Be(+) (n = 1-8) clusters. The HOMO-LUMO energy gaps as a function of the cluster size exhibit a pronounced even-odd alternation phenomenon. Sequently, the natural population analysis and polarizability for our systems have been analyzed and compared further.

In vivo near-realtime volumetric optical-resolution photoacoustic microscopy using a high-repetition-rate nanosecond fiber-laser

Optical-resolution photoacoustic microscopy (OR-PAM) is capable of achieving optical-absorption-contrast images with micron-scale spatial resolution. Previous OR-PAM systems have been frame-rate limited by mechanical scanning speeds and laser pulse repetition rate (PRR). We demonstrate OR-PAM imaging using a diode-pumped nanosecond-pulsed Ytterbium-doped 532-nm fiber laser with PRR up to 600 kHz. Combined with fast-scanning mirrors, our proposed system provides C-scan and 3D images with acquisition frame rate of 4 frames per second (fps) or higher, two orders of magnitude faster than previously published systems. High-contrast images of capillary-scale microvasculature in a live Swiss Webster mouse ear with ~6-µm optical lateral spatial resolution are demonstrated.

A systematic search for the structures, stabilities, and electronic properties of bimetallic Ca₂-doped gold clusters: comparison with pure gold clusters

The local meta-GGA exchange correlation density functional (TPSS) with a relativistic effective core potential was employed to systematically investigate the geometric structures, stabilities, and electronic properties of bimetallic Ca(2)Au( n ) (n = 1-9) and pure gold Au( n ) (n ≤ 11) clusters. The optimized geometries show that the most stable isomers for Ca(2)Au( n ) clusters have 3D structure when n > 2, and that one Au atom capping the Ca(2)Au( n-1) structure for different-sized Ca(2)Au( n ) (n = 1-9) clusters is the dominant growth pattern. The average atomic binding energies and second-order difference in energies show that the Ca(2)Au(4) isomer is the most stable among the Ca(2)Au( n ) clusters. The same pronounced even-odd alternations are found in the HOMO-LUMO gaps, VIPs, and hardnesses. The polarizabilities of the Ca(2)Au( n ) clusters show an obvious local minimum at n = 4. Moreover, the inverse corrections to the polarizabilities versus the ionization potential and hardness were found for the gold clusters.

Estimating optical absorption, scattering, and Grueneisen distributions with multiple-illumination photoacoustic tomography

While photoacoustic methods offer significant promise for high-resolution optical contrast imaging, quantification has thus far proved challenging. In this paper, a noniterative reconstruction technique for producing quantitative photoacoustic images of both absorption and scattering perturbations is introduced for the case when the optical properties of the turbid background are known and multiple optical illumination locations are used. Through theoretical developments and computational examples, it is demonstrated that multiple-illumination photoacoustic tomography (MI-PAT) can alleviate ill-posedness due to absorption-scattering nonuniqueness and produce quantitative high-resolution reconstructions of optical absorption, scattering, and Gruneisen parameter distributions. While numerical challenges still exist, we show that the linearized MI-PAT framework that we propose has orders of magnitude improved condition number compared with CW diffuse optical tomography.

Zinc accumulation and synthesis of ZnO nanoparticles using Physalis alkekengi L

A field survey and greenhouse experiments were conducted using Physalis alkekengi L. to investigate strategies of phytoremediation. In addition, ZnO nanoparticles were synthesized using P. alkekengi. P. alkekengi plants grew healthily at Zn levels from 50 to 5000 mg kg(-1) in soils. The plants incorporated Zn into their aerial parts (with mean dry weight values of 235-10,980 mg kg(-1)) and accumulated biomass (with a mean dry weight of 25.7 g plant(-1)) during 12 weeks. The synthesized ZnO nanoparticles showed a polydisperse behavior and had a mean size of 72.5 nm. The results indicate that P. alkekengi could be used for the remediation of zinc-contaminated soils. Moreover, the synthetic method of synthesizing ZnO nanoparticles from Zn hyperaccumulator plants constitutes a new insight into the recycling of metals in plant sources.

Comparison of different threshold values r for approximate entropy: application to investigate the heart rate variability between heart failure and healthy control groups

Approximate entropy (ApEn) is widely accepted as a complexity measure of the heart rate variability (HRV) signal, but selecting the criteria for the threshold value r is controversial. This paper aims to verify whether Chon's method of forecasting the r(max) is an appropriate one for the HRV signal. The standard limb lead ECG signals of 120 subjects were recorded for 10 min in a supine position. The subjects were divided into two groups: the heart failure (22 females and 38 males, median age 62.4 ± 12.6) and healthy control group (33 females and 27 males, median age 51.5 ± 16.9). Three types of ApEn were calculated: the ApEn(0.2) using the recommended constant r = 0.2, the ApEn(chon) using Chon's method and the ApEn(max) using the true r(max). A Wilcoxon rank sum test showed that the ApEn(0.2) (p = 0.267) and the ApEn(max) (p = 0.813) had no statistical differences between the two groups, while the ApEn(chon) (p = 0.040) had. We generated a synthetic database to study the effect of two influential factors (the signal length N and the ratio of short- and long-term variability sd(1)/sd(2)) on the empirical formula in Chon's method (Chon et al 2009 IEEE Eng. Med. Biol. Mag. 28 18-23). The results showed that the empirical formula proposed by Chon et al is a good method for analyzing the random signal, but not an appropriate tool for analyzing nonlinear signals, such as the logistic or HRV signals.

starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data

MicroRNAs (miRNAs) represent an important class of small non-coding RNAs (sRNAs) that regulate gene expression by targeting messenger RNAs. However, assigning miRNAs to their regulatory target genes remains technically challenging. Recently, high-throughput CLIP-Seq and degradome sequencing (Degradome-Seq) methods have been applied to identify the sites of Argonaute interaction and miRNA cleavage sites, respectively. In this study, we introduce a novel database, starBase (sRNA target Base), which we have developed to facilitate the comprehensive exploration of miRNA–target interaction maps from CLIP-Seq and Degradome-Seq data. The current version includes high-throughput sequencing data generated from 21 CLIP-Seq and 10 Degradome-Seq experiments from six organisms. By analyzing millions of mapped CLIP-Seq and Degradome-Seq reads, we identified ∼1 million Ago-binding clusters and ∼2 million cleaved target clusters in animals and plants, respectively. Analyses of these clusters, and of target sites predicted by 6 miRNA target prediction programs, resulted in our identification of approximately 400 000 and approximately 66 000 miRNA-target regulatory relationships from CLIP-Seq and Degradome-Seq data, respectively. Furthermore, two web servers were provided to discover novel miRNA target sites from CLIP-Seq and Degradome-Seq data. Our web implementation supports diverse query types and exploration of common targets, gene ontologies and pathways. The starBase is available at http://starbase.sysu.edu.cn/.

ncRNAimprint: a comprehensive database of mammalian imprinted noncoding RNAs

Imprinted noncoding RNAs (ncRNAs) are expressed mono-allelically in a parent-of-origin-dependent manner, which is mainly evident in mammals. Lying at a crossroad between imprinted genes and ncRNAs, imprinted ncRNAs show distinct features. They are likely to function in nontraditional ways compared to non-imprinted ncRNAs, and are much more responsible for the mechanism of genomic imprinting compared to imprinted protein-coding genes. An increasing number of human diseases have been shown to be related to abnormalities in imprinted ncRNAs. Due to their functional importance, many studies focusing on imprinted ncRNAs have been published in recent years; however, there is no systematic collection or description of imprinted ncRNAs and the rapidly growing knowledge is scattered in various places. Here, we describe a new database, ncRNAimprint, which serves as a comprehensive resource center for mammalian imprinted ncRNAs. A catalog of imprinted ncRNAs, including snoRNAs, microRNAs, piRNAs, siRNAs, antisense ncRNAs, and mRNA-like ncRNAs, was annotated in detail using information extracted from relevant literature and databases. Comprehensive collections of imprinted ncRNA-related diseases, imprinting control regions (ICRs), and imprinted regions were manually compiled to provide resources for current research focusing on imprinted ncRNAs. Small RNA deep sequencing reads that fully matched within imprinted regions were also included to offer useful evidence in detecting novel imprinted ncRNAs and to aid in analyzing expression patterns of known imprinted ncRNAs. A search page including four effective search forms and two graphical browsers was created for rapid retrieval and visualization of these data. The imprinted ncRNA database is freely accessible at http://rnaqueen.sysu.edu.cn/ncRNAimprint.

Magnetic resonance imaging and pituitary function in children with panhypopituitarism

BACKGROUND

To explore the relationship between magnetic resonance imaging (MRI) findings and multiple pituitary-target hormones in patients with panhypopituitarism or multiple pituitary hormone deficiency (MPHD).

METHODS

125 patients with MPHD (102 boys, MPHD group) and 90 age-, sex- and Tanner stage-matched normal children (control group) were enrolled. 96 of the patients with MPHD underwent MRI scans of the hypothalamic-pituitary area. The patients were subdivided into five stages according to their MRI findings. The serum concentrations of GH, IGF-1, FT(4), TSH, ACTH, cortisol, FSH, LH, prolactin, testosterone and estradiol were measured in patients and in controls.

RESULTS

MRI stage was significantly positively correlated with the number of pituitary hormone deficiencies (r = 0.9, p < 0.001). MRI stage was negatively correlated with peak GH, IGF-1, FT(4), cortisol and anterior pituitary height (r = -0.43, -0.47, -0.67, -0.54, and -0.49, respectively, p < 0.01). Diabetes insipidus patients could be stratified according to their MRI stage; diabetes insipidus was found mainly in patients with absence of the posterior pituitary bright spot or small ectopic posterior pituitary bright spot on MRI.

CONCLUSION

An abnormal MRI finding is evidence of MPHD and, correspondingly, there is a noteworthy correlation between MRI and pituitary function.

Deep sequencing of human nuclear and cytoplasmic small RNAs reveals an unexpectedly complex subcellular distribution of miRNAs and tRNA 3' trailers

BACKGROUND

MicroRNAs (miRNAs) are approximately 22-nt small non-coding regulatory RNAs that have generally been considered to regulate gene expression at the post-transcriptional level in the cytoplasm. However, recent studies have reported that some miRNAs localize to and function in the nucleus.

METHODOLOGY/PRINCIPAL FINDINGS

To determine the number of miRNAs localized to the nucleus, we systematically investigated the subcellular distribution of small RNAs (sRNAs) by independent deep sequencing sequenced of the nuclear and cytoplasmic pools of 18- to 30-nucleotide sRNAs from human cells. We identified 339 nuclear and 324 cytoplasmic known miRNAs, 300 of which overlap, suggesting that the majority of miRNAs are imported into the nucleus. With the exception of a few miRNAs evidently enriched in the nuclear pool, such as the mir-29b, the ratio of miRNA abundances in the nuclear fraction versus in the cytoplasmic fraction vary to some extent. Moreover, our results revealed that a large number of tRNA 3' trailers are exported from the nucleus and accumulate in the cytoplasm. These tRNA 3' trailers accumulate in a variety of cell types, implying that the biogenesis of tRNA 3' trailers is conserved and that they have a potential functional role in vertebrate cells.

CONCLUSION/SIGNIFICANCE

Our results provide the first comprehensive view of the subcellular distribution of diverse sRNAs and new insights into the roles of miRNAs and tRNA 3' trailers in the cell.

deepBase: a database for deeply annotating and mining deep sequencing data

Advances in high-throughput next-generation sequencing technology have reshaped the transcriptomic research landscape. However, exploration of these massive data remains a daunting challenge. In this study, we describe a novel database, deepBase, which we have developed to facilitate the comprehensive annotation and discovery of small RNAs from transcriptomic data. The current release of deepBase contains deep sequencing data from 185 small RNA libraries from diverse tissues and cell lines of seven organisms: human, mouse, chicken, Ciona intestinalis, Drosophila melanogaster, Caenhorhabditis elegans and Arabidopsis thaliana. By analyzing ∼14.6 million unique reads that perfectly mapped to more than 284 million genomic loci, we annotated and identified ∼380 000 unique ncRNA-associated small RNAs (nasRNAs), ∼1.5 million unique promoter-associated small RNAs (pasRNAs), ∼4.0 million unique exon-associated small RNAs (easRNAs) and ∼6 million unique repeat-associated small RNAs (rasRNAs). Furthermore, 2038 miRNA and 1889 snoRNA candidates were predicted by miRDeep and snoSeeker. All of the mapped reads can be grouped into about 1.2 million RNA clusters. For the purpose of comparative analysis, deepBase provides an integrative, interactive and versatile display. A convenient search option, related publications and other useful information are also provided for further investigation. deepBase is available at: http://deepbase.sysu.edu.cn/.

SnoRNAs from the filamentous fungus Neurospora crassa: structural, functional and evolutionary insights

BACKGROUND

SnoRNAs represent an excellent model for studying the structural and functional evolution of small non-coding RNAs involved in the post-transcriptional modification machinery for rRNAs and snRNAs in eukaryotic cells. Identification of snoRNAs from Neurospora crassa, an important model organism playing key roles in the development of modern genetics, biochemistry and molecular biology will provide insights into the evolution of snoRNA genes in the fungus kingdom.

RESULTS

Fifty five box C/D snoRNAs were identified and predicted to guide 71 2'-O-methylated sites including four sites on snRNAs and three sites on tRNAs. Additionally, twenty box H/ACA snoRNAs, which potentially guide 17 pseudouridylations on rRNAs, were also identified. Although not exhaustive, the study provides the first comprehensive list of two major families of snoRNAs from the filamentous fungus N. crassa. The independently transcribed strategy dominates in the expression of box H/ACA snoRNA genes, whereas most of the box C/D snoRNA genes are intron-encoded. This shows that different genomic organizations and expression modes have been adopted by the two major classes of snoRNA genes in N. crassa . Remarkably, five gene clusters represent an outstanding organization of box C/D snoRNA genes, which are well conserved among yeasts and multicellular fungi, implying their functional importance for the fungus cells. Interestingly, alternative splicing events were found in the expression of two polycistronic snoRNA gene hosts that resemble the UHG-like genes in mammals. Phylogenetic analysis further revealed that the extensive separation and recombination of two functional elements of snoRNA genes has occurred during fungus evolution.

CONCLUSION

This is the first genome-wide analysis of the filamentous fungus N. crassa snoRNAs that aids in understanding the differences between unicellular fungi and multicellular fungi. As compared with two yeasts, a more complex pattern of methylation guided by box C/D snoRNAs in multicellular fungus than in unicellular yeasts was revealed, indicating the high diversity of post-transcriptional modification guided by snoRNAs in the fungus kingdom.

Postoperative pituitary hormonal disturbances and hormone replacement therapy time and dosage in children with craniopharyngiomas

BACKGROUND

The proliferative activity and penetration into the hypothalamic structures in children craniopharyngiomas (CP) often make radical resection difficult. Therefore, complete resection of CP often results in permanent multiple pituitary hormone deficiency (MPHD). This study aimed to elucidate the postoperative pituitary hormonal disturbances, and hormone replacement therapy (HRT) time and dosage in children with CP.

METHODS

Twenty patients with growth retardation and CP after resection, comprising 14 boys and 6 girls, with a mean age of (10.63 +/- 3.18) years (Group A) and 10 male patients of group A aged > 10 years (Group B) were entolled. Thirty age-, sex- and Tanner stage-matched normal children (control Group A), and 44 male older children > 10 years (control Group B) served as controls. The serum concentrations of insulin-like growth factor-1 (IGF-1), growth hormone (GH), free thyroxine (FT4), thyroid-stimulating hormone (TSH), adrenocorticortropic hormone (ACTH), cortisol (COR), follicle stimulating hormone (FSH), luteinizing hormone (LH), prolactin (PRL), testosterone (T) and estradiol (E2) were measured in the CP patients after resection and in controls. The appropriate time and dosage of HRT were investigated. Linear correlation analysis was made between levothyroxine (L-T4) dosage and primary FT4 in CP patients after resection.

RESULTS

All cases had MPHD. The serum peak GH, IGF-1, FT4 and COR levels of Group A were significantly lower than that of the control Group A. The serum IGF-1 concentration increased to the normal level after 3 months of rhGH therapy; the serum FSH, LH, and T levels were significantly decreased (P < 0.001); however, E2 and PRL were significantly increased (P < 0.001) in Group B compared with the control Group B; 18 cases were found to have central diabetes insipidus (DI) by water deprivation test and MRI. There was a significant negative linear regression (r = -0.8, P < 0.001) between L-T4 and primary FT4 in Group A patients with CP after resection, giving a regression equation of L-T4 dosage (microg.kg(-1).d(-1)) = 3.5-0.2 x FT4 (microg.kg(-1).d(-1)). The time and corresponding dosage of HRT for CP after resection were: rhGH started 1 year after resection and no recurrence of CP on MRI, when IGF-1 reached the normal range, the rhGH dosage was (0.13 +/- 0.04) U.kg(-1).d(-1); hydrocortisone (H-C) was started as soon as possible, and was kept in the lower normal range, at a dosage of (12.6 +/- 4.8) mg/m2; levothyroxine started after H-C or at the same time to maintain FT4 in the higher normal range, at a dosage of (1.65 +/- 0.70) microg.kg(-1).d(-1); Minirin (DDAVP) was started as soon as possible, elicited no symptoms, and maintained normal electrolyte levels; the dosage was (0.16 +/- 0.04) mg/m2.

CONCLUSION

Patients with CP after resection often displayed MPHD, and needed total HRT at appropriate time and dosage to improve the quality of life and normal growth.

Transcriptional regulation of fatty acid translocase/CD36 expression by CCAAT/enhancer-binding protein alpha

Fatty acid translocase (FAT/CD36) plays an important role in facilitating long chain fatty acid transport. FAT/CD36 gene deletion protects mice from high fat diet-induced obesity. In this study we have investigated the regulatory mechanism of FAT/CD36 expression at the transcription level. FAT/CD36 expression was activated during 3T3-L1 adipocyte differentiation, and FAT/CD36 protein levels were positively correlated with CCAAT/enhancer-binding protein alpha (C/EBPalpha) and peroxisome proliferator-activated receptor gamma. However, a negative correlation was detected between FAT/CD36 and C/EBPbeta. Overexpression of C/EBPalpha or C/EBPbeta increased FAT/CD36 mRNA and protein levels in several types of cells. Restoration of C/EBPalpha or C/EBPbeta expression in C/EBPalpha- or C/EBPbeta-deficient mouse embryonic fibroblasts increased FAT/CD36 expression. However, in mouse embryonic fibroblasts C/EBPalpha was a more potent activator of FAT/CD36 expression than was C/EBPbeta. Expression of C/EBPalpha robustly increased FAT/CD36 proximal promoter-directed luciferase expression in human embryonic kidney 293 cells. A C/EBP-responsive element was identified in the FAT/CD36 promoter by using 5' and specific site mutations. The binding of C/EBPalpha in the FAT/CD36 promoter was detected by chromatin immunoprecipitation in 3T3-L1 adipocytes. These results demonstrated that C/EBPalpha regulates FAT/CD36 gene expression at the transcriptional level.

Regulation on maturation and function of dendritic cells by Astragalus mongholicus polysaccharides

Astragalus mongholicus polysaccharides(ASP) isolated from one of the Chinese herbs-A. mongholicus which are known to have a variety of immunomodulatory activity. However, little is known about their immunomodulatory effects on murine bone marrow (BM)-derived dendritic cells (DC). DC are professional antigen presenting cells, which are pivotal for initiation of primary immune response. In this study, the regulatory effects of ASP on maturation and function of cultured murine BM-derived DC were investigated in vitro. ASP (10, 50, 100, 250 microg/ml) could increase the co-expression of CD-11c and MHC class II molecules on DC surface, and the 100 microg/ml is the optimal dose. The ability of unstimulated DC to uptake FITC-dextran was higher than that of ASP- or LPS-treated DC. We analyzed the concentration of IL-12 secreted by DC using ELISA. ASP-treated DC secreted a higher level of IL-12 than untreated DC. And ASP- or LPS-treated DC displayed a more mature morphology, with long protrusions, while untreated-DC displayed shorter protrusions than stimulated DC.