Integration genetic linkage map construction and several potential QTLs mapping of Chinese shrimp (Fenneropenaeus chinensis) based on three types of molecular markers

In this study, totally 54 selected polymorphic SSR loci of Chinese shrimp (Fenneropenaeus chinensis), in addition with the previous linkage map of AFLP and RAPD markers, were used in consolidated linkage maps that composed of SSR, AFLP and RAPD markers of female and male construction, respectively. The female linkage map contained 236 segregating markers, which were linked in 44 linkage groups, and the genome coverage was 63.98%. The male linkage map contained 255 segregating markers, which were linked in 50 linkage groups, covering 63.40% of F. chinensis genome. There were nine economically important traits and phenotype characters of F. chinensis were involved in QTL mapping using multiple-QTL mapping strategy. Five potential QTLs associated with standard length (q-standardl-01), with cephalothorax length (q-cephal-01), with cephaloghorax width (q-cephaw-01), with the first segment length (q-firsel-01) and with anti-WSSV (q-antiWSSV-01) were detected on female LG1 and male LG44 respectively with LOD> 2.5. The QTL q-firsel-01 was at 73.603 cM of female LG1. Q-antiWSSV-01 was at 0 cM of male LG44. The variance explained of these five QTLs was from 19.7-33.5% and additive value was from -15.9175 to 7.3675. The closest markers to these QTL were all SSR, which suggested SSR marker was superior to AFLP and RAPD in the QTL mapping.

β-Galactosidase with transgalactosylation activity from Lactobacillus fermentum K4

The LacLM β-galactosidase of Lactobacillus fermentum K4 is encoded by 2 consecutive genes, lacL (large subunit) and lacM (small subunit), that share 17 overlapping nucleotides. Phylogenetic analysis revealed that this enzyme was closely related to other Lactobacillus β-galactosidases and provided significant insight into its common and distinct characteristics. We cloned both the lacL and lacM genes of L. fermentum K4 and heterologously expressed each in Escherichia coli, although the recombinant enzyme was only functional when both were expressed on the same plasmid. We evaluated the enzymatic properties of this species-specific LacLM β-galactosidase and discovered that it acts as both a hydrolase, bioconverting lactose into glucose and galactose, and a transgalactosylase, generating prebiotic galacto-oligosaccharides (GOS). The recombinant β-galactosidase showed a broad pH optimum and stability around neutral pH. The optimal temperature and Michaelis constant (K(m)) for the substrates o-nitrophenyl-β-D-galactopyranoside and lactose were, respectively, 40°C and 45 to 50°C and 1.31 mM and 27 mM. The enzyme activity was stimulated by some cations such as Na⁺, K⁺, and Mg²⁺. In addition, activity was also enhanced by ethanol (15%, wt/vol). The transgalactosylation activity of L. fermentum K4 β-galactosidase effectively and rapidly generated GOS, up to 37% of the total sugars from the reaction. Collectively, our results suggested that the β-galactosidase from L. fermentum K4 could be exploited for the formation of GOS.

Impact of ligand and protein desolvation on ligand binding to the S1 pocket of thrombin

In the present study, we investigate the impact of a tightly bound water molecule on ligand binding in the S1 pocket of thrombin. The S1 pocket contains a deeply buried deprotonated aspartate residue (Asp189) that is, due to its charged state, well hydrated in the uncomplexed state. We systematically studied the importance of this water molecule by evaluating a series of ligands that contains pyridine-type P1 side chains that could potentially alter the binding properties of this water molecule. All of the pyridine derivatives retain the original hydration state albeit sometimes with a slight perturbance. In order to prevent a direct H-bond formation with Asp189, and to create a permanent positive charge on the P1 side chain that is positioned adjacent to the Asp189 carboxylate anion, we methylated the pyridine nitrogen. This methylation resulted in displacement of water but was accompanied by a loss in binding affinity. Quantum chemical calculations of the ligand solvation free energy showed that the positively charged methylpyridinium derivatives suffer a large penalty of desolvation upon binding. Consequently, they have a substantially less favorable enthalpy of binding. In addition to the ligand desolvation penalty, the hydration shell around Asp189 has to be overcome, which is achieved in nearly all pyridinium derivatives. Only for the ortho derivative is a partial population of a water next to Asp189 found. Possibly, the gain of electrostatic interactions between the charged P1 side chain and Asp189 helps to compensate for the desolvation penalty. In all uncharged pyridine derivatives, the solvation shell remains next to Asp189, partly mediating interactions between ligand and protein. In the case of the para-pyridine derivative, a strongly disordered cluster of water sites is observed between ligand and Asp189.

Observation of electronic Raman scattering in metallic carbon nanotubes

We present experimental measurements of the electronic contribution to the Raman spectra of individual metallic single-walled carbon nanotubes (MSWNTs). Photoexcited carriers are inelastically scattered by a continuum of low-energy electron-hole pairs created across the graphenelike linear electronic subbands of the MSWNTs. The optical resonances in MSWNTs give rise to well-defined electronic Raman peaks. This resonant electronic Raman scattering is a unique feature of the electronic structure of these one-dimensional quasimetals.

Improved diabetes control in the elderly delays global cognitive decline

OBJECTIVES

To examine whether improved diabetes control is related to better cognitive outcomes.

DESIGN

Randomized control trial.

SETTING

A randomized trial of telemedicine vs. usual care in elderly persons with type 2 diabetes.

PARTICIPANTS

Participants were 2169 persons 55 years and older with type 2 diabetes from New York City and Upstate New York.

INTERVENTION

The diabetes case management intervention was implemented by a diabetes nurse, via a telemedicine unit in the participant's home, and in coordination with the primary care physician.

MEASUREMENTS

Hemoglobin A1c (HbA1c), systolic blood pressure (SBP), and low density lipoprotein cholesterol (LDL), were measured at a baseline visit and at up to 5 annual follow-up visits. Global cognition was measured at those visits with the Comprehensive Assessment and Referral Evaluation (CARE).

RESULT

In mixed models the intervention was related to slower global cognitive decline in the intervention group (p = 0.01). Improvements in HbA1c (p = 0.03), but not SBP or LDL, mediated the effect of the intervention on cognitive decline.

CONCLUSION

Improved diabetes control in the elderly following existing guidelines through a telemedicine intervention was associated with less global cognitive decline. The main mediator of this effect seemed to be improvements in HbA1c.

Single-layer behavior and its breakdown in twisted graphene layers

We report high magnetic field scanning tunneling microscopy and Landau level spectroscopy of twisted graphene layers grown by chemical vapor deposition. For twist angles exceeding ~3° the low energy carriers exhibit Landau level spectra characteristic of massless Dirac fermions. Above 20° the layers effectively decouple and the electronic properties are indistinguishable from those in single-layer graphene, while for smaller angles we observe a slowdown of the carrier velocity which is strongly angle dependent. At the smallest angles the spectra are dominated by twist-induced van Hove singularities and the Dirac fermions eventually become localized. An unexpected electron-hole asymmetry is observed which is substantially larger than the asymmetry in either single or untwisted bilayer graphene.

Epidemiological Investigation of Metabolic Syndrome and Analysis of Relevant Factors in North-Eastern China

This epidemiological study was conducted to investigate the prevalence of metabolic syndrome and associated risk factors in Chinese subjects from Dehui in northeastern China. Using a random sampling method, a questionnaire was completed by 3785 permanent residents aged 18-72 years and relevant clinical data were collected from each subject. Binary multivariate logistic regression analysis was used to identify factors that were significantly associated with metabolic syndrome. Based on the International Diabetes Federation definition, the prevalence of metabolic syndrome was 22.4%, which is higher than that of the general Chinese population. Metabolic syndrome occurred more frequently in females and the prevalence gradually increased with age. Living in an urban setting and being female, > 50 years old, overweight, having total cholesterol ≥ 5.18 mmol/l, low-density lipoprotein cholesterol ≥ 3.1 mmol/l, and a fatty liver were significant risk factors associated with metabolic syndrome.

Identification and characterization of the two-component cell lysis cassette encoded by temperate bacteriophage phiPYB5 of Lactobacillus fermentum

AIMS

To characterize the two-component cell lysis cassette comprised of holin (Hyb5) and endolysin (Lyb5) encoded by Lactobacillus fermentum temperate bacteriophage phiPYB5, and illustrate the potential application of Lyb5 as therapeutic agents.

METHODS AND RESULTS

The hyb5-lyb5 cassette was cloned from the genome library of phiPYB5, and the hyb5, lyb5 and hyb5-lyb5 cassette were expressed in E. coli BL21, respectively. The molecular weight of Hyb5 indicated by SDS-PAGE was 19 kDa, and Lyb5 was 45 kDa. Both Hyb5 and Lyb5 protein could induce cell lysis alone, resulting in the leakage of beta-galactosidase. However, the Hyb5-Lyb5 cassette lysed the host cells more rapidly and extensively. By zymogram analysis, Lyb5 exhibited a broad lytic spectrum.

CONCLUSIONS

Overexpression of hyb5, lyb5 and hyb5-lyb5 cassette were carried out in E. coli and Lyb5 exhibited a broad lytic spectrum.

SIGNIFICANCE AND IMPACT OF THE STUDY

The Lyb5 produced in E. coli exhibited a broad lytic spectrum against Gram-positive strains including Staphylococcus aureus as well as Gram-negative strains such as Salmonella typhi, suggesting that Lyb5 provides a potential alternative of diagnostic tools and therapeutic agents.

Computer-aided Prognosis of Neuroblastoma on Whole-slide Images: Classification of Stromal Development

We are developing a computer-aided prognosis system for neuroblastoma (NB), a cancer of the nervous system and one of the most malignant tumors affecting children. Histopathological examination is an important stage for further treatment planning in routine clinical diagnosis of NB. According to the International Neuroblastoma Pathology Classification (the Shimada system), NB patients are classified into favorable and unfavorable histology based on the tissue morphology. In this study, we propose an image analysis system that operates on digitized H&E stained whole-slide NB tissue samples and classifies each slide as either stroma-rich or stroma-poor based on the degree of Schwannian stromal development. Our statistical framework performs the classification based on texture features extracted using co-occurrence statistics and local binary patterns. Due to the high resolution of digitized whole-slide images, we propose a multi-resolution approach that mimics the evaluation of a pathologist such that the image analysis starts from the lowest resolution and switches to higher resolutions when necessary. We employ an offine feature selection step, which determines the most discriminative features at each resolution level during the training step. A modified k-nearest neighbor classifier is used to determine the confidence level of the classification to make the decision at a particular resolution level. The proposed approach was independently tested on 43 whole-slide samples and provided an overall classification accuracy of 88.4%.

Computer-aided evaluation of neuroblastoma on whole-slide histology images: Classifying grade of neuroblastic differentiation

Neuroblastoma (NB) is one of the most frequently occurring cancerous tumors in children. The current grading evaluations for patients with this disease require pathologists to identify certain morphological characteristics with microscopic examinations of tumor tissues. Thanks to the advent of modern digital scanners, it is now feasible to scan cross-section tissue specimens and acquire whole-slide digital images. As a result, computerized analysis of these images can generate key quantifiable parameters and assist pathologists with grading evaluations. In this study, image analysis techniques are applied to histological images of haematoxylin and eosin (H&E) stained slides for identifying image regions associated with different pathological components. Texture features derived from segmented components of tissues are extracted and processed by an automated classifier group trained with sample images with different grades of neuroblastic differentiation in a multi-resolution framework. The trained classification system is tested on 33 whole-slide tumor images. The resulting whole-slide classification accuracy produced by the computerized system is 87.88%. Therefore, the developed system is a promising tool to facilitate grading whole-slide images of NB biopsies with high throughput.

Softening of the radial breathing mode in metallic carbon nanotubes

The softening of the radial breathing mode (RBM) of metallic single walled carbon nanotubes (m-SWNTs) due to electron-phonon coupling has been studied by observing the Fermi level [see text] dependence of the RBM Raman peak. In situ Raman spectra were obtained from several individual m-SWNTs while varying [see text] electrochemically. The RBM frequency of an intrinsic m-SWNT is shown to be down-shifted relative to highly doped tubes by approximately 2 cm(1). The down-shift is greatest for small diameter and small chiral angle SWNTs. Most tubes show no change in RBM linewidth. A comparison is drawn between the RBM and the G band (A(LO) phonon) with respect to the [see text] dependence of their frequencies and linewidths.

Raman spectroscopy study of isolated double-walled carbon nanotubes with different metallic and semiconducting configurations

A double-walled carbon nanotube (DWNT) provides the simplest system to study the interaction between concentric layers in carbon nanotubes. The inner and outer walls of a DWNT can be metallic (M) or semiconducting (S), and each of the four possible configurations (M@M, M@S, S@S, S@M) has different electronic properties. Here we report, for the first time, detailed Raman spectroscopy experiments carried out on individual DWNTs, where both concentric tubes are measured under resonance conditions, in order to understand the dependence of their electronic and optical properties according to their configuration. Interestingly, for the three DWNTs that were studied, the inner-outer tube distance (e.g., 0.31-0.33 nm) was less than the interlayer spacing in graphite. We believe these results have important implications in the fabrication of electronic devices using different types of S and M tubular interconnects.

Competition between the spring force constant and the phonon energy renormalization in electrochemically doped semiconducting single-walled carbon nanotubes

A detailed analysis of the in situ Raman spectroelectrochemical behavior of individual semiconducting single-walled carbon nanotubes (SWCNTs) is presented. Special attention has been paid to the development of the tangential (TG) mode frequency, which shifts when the externally applied potential Ve is shifted away from Ve=0. The magnitude and direction (upshift or downshift) of the tangential mode band has been found to be dependent on the diameter of the semiconducting tubes. For negative charging, the small-diameter tubes exhibit a downshift while the large-diameter tubes exhibit an upshift. This behavior is explained by a competition between two effects which cause opposite shifts in the TG mode frequency during negative charging: a phonon renormalization effect and a C-C bond weakening during the charging process. Positive charging always causes an upshift of the TG mode frequency. However, the magnitude of the upshift is dependent on the tube diameter.

Correction of the disease phenotype in the mouse model of Stargardt disease by lentiviral gene therapy

Autosomal recessive Stargardt disease (STGD1) is a macular dystrophy caused by mutations in the ABCA4 (ABCR) gene. The disease phenotype that is most recognized in STGD1 patients, and also in the Abca4-/- mouse (a disease model), is lipofuscin accumulation in retinal pigment epithelium. Here, we tested whether delivery of the normal (wt) human ABCA4 gene to the subretinal space of the Abca4 -/- mice via lentiviral vectors would correct the disease phenotype; that is, reduce accumulation of the lipofuscin pigment A2E. Equine infectious anemia virus (EIAV)-derived lentiviral vectors were constructed expressing either the human ABCA4 gene or the LacZ reporter gene under the control of the constitutive (CMV) or photoreceptor-specific (Rho) promoters. Abca4-/- mice were injected subretinally with 1 microl ( approximately 5.0 x 10(5) TU) of each EIAV vector in one eye at postnatal days 4 and 5. An injection of saline, an EIAV-null vector, or an uninjected contralateral eye served as a control. Mice were killed at various times after injection to determine photoreceptor (PR) transduction efficiency and A2E concentrations. EIAV-LacZ vectors transduced from 5 to 20% of the PRs in the injected area in mice. Most importantly, a single subretinal injection of EIAV-CMV-ABCA4 to Abca4-/- mouse eyes substantially reduced disease-associated A2E accumulation compared to untreated and mock-treated control eyes. Treated eyes of Abca4-/- mice accumulated 8-12 pmol per eye (s.d.=2.7) of A2E 1 year after treatment, amounts comparable to wt controls, whereas mock-treated or untreated eyes had 3-5 times more A2E (27-39 pmol per eye, s.d.=1.5; P=0.001-0.005). Although extrapolation to humans requires caution, the high transduction efficiency of both rod and cone photoreceptors and the statistically significant reduction of A2E accumulation in the mouse model of STGD1 suggest that lentiviral gene therapy is a potentially efficient tool for treating ABCA4-associated diseases.