Dynamics of Proofreading by the E. coli Pol III Replicase

The αɛθ core of Escherichia coli DNA polymerase III (Pol III) associates with the β₂ sliding clamp to processively synthesize DNA and remove misincorporated nucleotides. The α subunit is the polymerase while ɛ is the 3' to 5' proofreading exonuclease. In contrast to the polymerase activity of Pol III, dynamic features of proofreading are poorly understood. We used single-molecule assays to determine the excision rate and processivity of the β₂-associated Pol III core, and observed that both properties are enhanced by mutational strengthening of the interaction between ɛ and β₂. Thus, the ɛ-β₂ contact is maintained in both the synthesis and proofreading modes. Remarkably, single-molecule real-time fluorescence imaging revealed the dynamics of transfer of primer-template DNA between the polymerase and proofreading sites, showing that it does not involve breaking of the physical interaction between ɛ and β₂.

Error rate of automated calculation for wound surface area using a digital photography

BACKGROUND

Although measuring would size using digital photography is a quick and simple method to evaluate the skin wound, the possible compatibility of it has not been fully validated.

PURPOSE

To investigate the error rate of our newly developed wound surface area calculation using digital photography.

METHODS

Using a smartphone and a digital single lens reflex (DSLR) camera, four photographs of various sized wounds (diameter: 0.5-3.5 cm) were taken from the facial skin model in company with color patches. The quantitative values of wound areas were automatically calculated. The relative error (RE) of this method with regard to wound sizes and types of camera was analyzed.

RESULTS

RE of individual calculated area was from 0.0329% (DSLR, diameter 1.0 cm) to 23.7166% (smartphone, diameter 2.0 cm). In spite of the correction of lens curvature, smartphone has significantly higher error rate than DSLR camera (3.9431±2.9772 vs 8.1303±4.8236). However, in cases of wound diameter below than 3 cm, REs of average values of four photographs were below than 5%. In addition, there was no difference in the average value of wound area taken by smartphone and DSLR camera in those cases.

CONCLUSION

For the follow-up of small skin defect (diameter: <3 cm), our newly developed automated wound area calculation method is able to be applied to the plenty of photographs, and the average values of them are a relatively useful index of wound healing with acceptable error rate.

Optimization of electrospun fibrous membranes for in vitro modeling of blood-brain barrier

The blood-brain barrier (BBB) plays a critical role in brain homeostasis at the cellular and global level. Mimicking the selective permeability and transport properties of the BBB to specific molecules and cells remains a significant challenge towards the development of a physiologically relevant in vitro BBB model. In this study, we developed electrospun poly (ε-caprolactone) (PCL) and polyethylene glycol (PEG) copolymer membranes that supported different cellular components of the neurovascular unit including human-derived endothelial cells, pericytes and astrocytes. Comparative analyses of thickness, morphology, biocompatibility and permeability of membranes were also conducted. We found that collagen coated 4%PEG-96%PCL membranes supported the growth of a confluent and tight endothelium confirmed by transendothelial electrical resistance measurements (TEER). Based on fabrication process and reported results, we finally discuss the adoption of these electrospun fiber membranes for in vitro and on-a-chip human BBB models.

Light-Induced Fluorescence Modulation of Quantum Dot-Crystal Violet Conjugates: Stochastic Off-On-Off Cycles for Multicolor Patterning and Super-Resolution

Photoswitching or modulation of quantum dots (QDs) can be promising for many fields that include display, memory, and super-resolution imaging. However, such modulations have mostly relied on photomodulations of conjugated molecules in QD vicinity, which typically require high power of high energy photons at UV. We report a visible light-induced facile modulation route for QD-dye conjugates. QD crystal violets conjugates (QD-CVs) were prepared and the crystal violet (CV) molecules on QD quenched the fluorescence efficiently. The fluorescence of QD-CVs showed a single cycle of emission burst as they go through three stages of (i) initially quenched "off" to (ii) photoactivated "on" as the result of chemical change of CVs induced by photoelectrons from QD and (iii) back to photodarkened "off" by radical-associated reactions. Multicolor on-demand photopatterning was demonstrated using QD-CV solid films. QD-CVs were introduced into cells, and excitation with visible light yielded photomodulation from "off" to "on" and "off" by nearly ten fold. Individual photoluminescence dynamics of QD-CVs was investigated using fluorescence correlation spectroscopy and single QD emission analysis, which revealed temporally stochastic photoactivations and photodarkenings. Exploiting the stochastic fluorescence burst of QD-CVs, simultaneous multicolor super-resolution localizations were demonstrated.

The bent conformation of poly(A)-binding protein induced by RNA-binding is required for its translational activation function

A recent study revealed that poly(A)-binding protein (PABP) bound to poly(A) RNA exhibits a sharply bent configuration at the linker region between RNA-recognition motif 2 (RRM2) and RRM3, whereas free PABP exhibits a highly flexible linear configuration. However, the physiological role of the bent structure of mRNA-bound PABP remains unknown. We investigated a role of the bent structure of PABP by constructing a PABP variant that fails to form the poly(A)-dependent bent structure but maintains its poly(A)-binding activity. We found that the bent structure of PABP/poly(A) complex is required for PABP's efficient interaction with eIF4G and eIF4G/eIF4E complex. Moreover, the mutant PABP had compromised translation activation function and failed to augment the formation of 80S translation initiation complex in an in vitro translation system. These results suggest that the bent conformation of PABP, which is induced by the interaction with 3′ poly(A) tail, mediates poly(A)-dependent translation by facilitating the interaction with eIF4G and the eIF4G/eIF4E complex. The preferential binding of the eIF4G/eIF4E complex to the bent PABP/poly(A) complex seems to be a mechanism discriminating the mRNA-bound PABPs participating in translation from the idling mRNA-unbound PABPs.

Cascading MutS and MutL sliding clamps control DNA diffusion to activate mismatch repair

Mismatched nucleotides arise from polymerase misincorporation errors, recombination between heteroallelic parents and chemical or physical DNA damage. Highly conserved MutS (MSH) and MutL (MLH/PMS) homologues initiate mismatch repair and, in higher eukaryotes, act as DNA damage sensors that can trigger apoptosis. Defects in human mismatch repair genes cause Lynch syndrome or hereditary non-polyposis colorectal cancer and 10-40% of related sporadic tumours. However, the collaborative mechanics of MSH and MLH/PMS proteins have not been resolved in any organism. We visualized Escherichia coli (Ec) ensemble mismatch repair and confirmed that EcMutS mismatch recognition results in the formation of stable ATP-bound sliding clamps that randomly diffuse along the DNA with intermittent backbone contact. The EcMutS sliding clamps act as a platform to recruit EcMutL onto the mismatched DNA, forming an EcMutS-EcMutL search complex that then closely follows the DNA backbone. ATP binding by EcMutL establishes a second long-lived DNA clamp that oscillates between the principal EcMutS-EcMutL search complex and unrestricted EcMutS and EcMutL sliding clamps. The EcMutH endonuclease that targets mismatch repair excision only binds clamped EcMutL, increasing its DNA association kinetics by more than 1,000-fold. The assembly of an EcMutS-EcMutL-EcMutH search complex illustrates how sequential stable sliding clamps can modulate one-dimensional diffusion mechanics along the DNA to direct mismatch repair.

Lymph node size is not a reliable criterion for predicting nodal metastasis in rectal neuroendocrine tumours

AIM

The study was designed to assess the correlation between lymph node (LN) size and LN metastasis in patients with rectal neuroendocrine tumours (NETs).

METHOD

Forty patients who underwent curative resection with lymphadenectomy for a rectal NET between January 2007 and December 2012 were included. The short and long diameters of entire nodes were microscopically measured using a slide gauge.

RESULTS

In all, 1052 LNs were collected from the 40 patients, with 49 (4.7%) showing evidence of metastasis. Metastasis-positive LNs had significantly greater long and short diameters (P < 0.001) than metastasis-negative LNs. Of the 49 metastatic LNs, 29 (59.2%) were ≤ 5 mm in largest diameter. In five patients, the largest metastatic LN was only 2-3 mm in diameter. In clinically node-negative (cN0) patients, 18 (51.4%) patients had metastatic LNs (pN1).

CONCLUSION

The size of LNs containing metastasis varied widely, with some being very small. LN size alone is therefore not a sufficient predictor of tumour metastasis in rectal NETs. Radical surgery with lymphadenectomy should be considered for patients with rectal NETs with high risk factors for LN metastasis, even those without LN enlargement.

Retroviral intasomes search for a target DNA by 1D diffusion which rarely results in integration

Retroviruses must integrate their linear viral cDNA into the host genome for a productive infection. Integration is catalysed by the retrovirus-encoded integrase (IN), which forms a tetramer or octamer complex with the viral cDNA long terminal repeat (LTR) ends termed an intasome. IN removes two 3'-nucleotides from both LTR ends and catalyses strand transfer of the recessed 3'-hydroxyls into the target DNA separated by 4-6 bp. Host DNA repair restores the resulting 5'-Flap and single-stranded DNA (ssDNA) gap. Here we have used multiple single molecule imaging tools to determine that the prototype foamy virus (PFV) retroviral intasome searches for an integration site by one-dimensional (1D) rotation-coupled diffusion along DNA. Once a target site is identified, the time between PFV strand transfer events is 470 ms. The majority of PFV intasome search events were non-productive. These observations identify new dynamic IN functions and suggest that target site-selection limits retroviral integration.

An Efficient Site-Specific Method for Irreversible Covalent Labeling of Proteins with a Fluorophore

Fluorophore labeling of proteins while preserving native functions is essential for bulk Förster resonance energy transfer (FRET) interaction and single molecule imaging analysis. Here we describe a versatile, efficient, specific, irreversible, gentle and low-cost method for labeling proteins with fluorophores that appears substantially more robust than a similar but chemically distinct procedure. The method employs the controlled enzymatic conversion of a central Cys to a reactive formylglycine (fGly) aldehyde within a six amino acid Formylglycine Generating Enzyme (FGE) recognition sequence in vitro. The fluorophore is then irreversibly linked to the fGly residue using a Hydrazinyl-Iso-Pictet-Spengler (HIPS) ligation reaction. We demonstrate the robust large-scale fluorophore labeling and purification of E.coli (Ec) mismatch repair (MMR) components. Fluorophore labeling did not alter the native functions of these MMR proteins in vitro or in singulo. Because the FGE recognition sequence is easily portable, FGE-HIPS fluorophore-labeling may be easily extended to other proteins.

Reconstruction algorithm for nasal basal cell carcinoma with skin involvement only: analysis of 221 cases repaired by minor surgery

BACKGROUND

Basal cell carcinoma (BCC) often occurs on the nose. Reconstruction of the nose should yield excellent aesthetic and functional outcomes.

AIM

We propose a technical algorithm for the reconstruction of surgical defects, based on our analysis of 221 cases of nasal BCC with skin involvement only, which could be repaired by minor surgery.

METHODS

The aesthetic and functional outcomes for various reconstruction techniques were analysed according to defect location and size. A reconstruction algorithm was proposed with the aim of obtaining the best surgical results.

RESULTS

Defect location and size were key considerations. Primary closure was the first option for small defects (< 10 mm), with scores of 3.4 for objective aesthetic outcome (OAO), 3.2 for subjective aesthetic outcome (SAO) and 3.3 for subjective functional outcome (SFO). The first option for medium defects (1-20 mm) was the island pedicle flap, with scores of 3.5 for OAO, 3.2 for SAO and 3.7 for SFO. The first option for large defects (> 20 mm) was the transposition flap for the upper nose (scores of 2.0 for OAO and SAO and 3.0 for SFO) and the interpolation flap for the lower nose (2.8 for OAO and 2.9 for SAO and SFO).

CONCLUSIONS

We have proposed an algorithm to select the optimal technique for repairing nasal BCC surgical defects according to their size and location.

Antihypertensive effect of volume depletion: interrelation with renal prostaglandins

Since the original studies of Patak et al. in 1975 revealed that the antihypertensive and natriuretic effects of furosemide were markedly blunted or abrogated by indomethacin in both normotensive and hypertensive man, it has been postulated that the ameliorative effects of furosemide in human essential hypertension might be mediated by release of intrarenal prostaglandins. To study the direct effects of furosemide on prostaglandin biosynthesis and release, slices of rabbit renal medulla were incubated in Krebs-Ringer bicarbonate buffer, glucose 10 mM, 1-14C-arachidonic acid (AA) 10 microM, HSA /g/100 ml, 30 min 37 degrees C. Measurements were made of radioactive AA leads to PGE2, and total endogenous immunoreactive PGE2 production (iPGE2) with and without the addition of furosemide (10 microgram/ml) to the media. In the absence of furosemide AA leads to PGE2 was 73 +/- 22 nmol/30 min/g and in the presence of furosemide it fell to 30 +/- 4 nmol/30min/g. iPGE2 was 33 +/- / ng/30 min/mg and decreased to 25 +/- 3 mg with furosemide. These results indicate that the natriuresis and antihypertensive effect of furosemide in vivo, which is associated with a significant increase in urinary PGE2, is not the result of a direct stimulation of furosemide on prostaglandin synthesis but may result from a decrease in PGE metabolism, conversion to another biologically active prostaglandin or possibly be a reflection of events secondary to a direct effect of furosemide on renal hemodynamics and electrolyte excretion.

Lichen planus pemphigoides associated with chronic hepatitis B virus infection

Lichen planus pemphigoides (LPP) is a rare autoimmune dermatosis with the features of both lichen planus (LP) and bullous pemphigoid (BP). Although in rare cases, LPP has been associated with several medications and conditions, it is generally considered an idiopathic disorder, and its pathogenesis remains uncertain. We report a 56-year-old woman who presented with a 2-year history of flat-topped, polygonal, violaceous-colored papules and some bullae. She was diagnosed with chronic hepatitis B virus (HBV) infection, which had been treated intermittently with entecavir. Histopathological examination showed the typical features of LP with subepidermal blisters, and with linear deposits of IgG along the basement membrane zone on direct immunofluorescence. Immunoblotting revealed antibodies directed at the BP180 and BP230 antigens. We diagnosed the patient with LPP, and treated the condition with systemic steroids and dapsone. To our knowledge, this is the first report of LPP in a patient with chronic HBV infection.

Incidental renal cell carcinoma originating from a native kidney after en-bloc resection for adrenal carcinoma in a kidney transplant recipient

BACKGROUND

Renal transplantation is the best treatment for patients with end-stage renal disease. Although there is significantly increased risk of malignancy after renal transplantation, carcinoma of the native kidney is very rare, and moreover, the risk of endocrinologic malignancy after renal transplantation is lower than in the general population and adrenal cortical carcinoma extremely rare. We report a case of incidental renal cell carcinoma originating from a native kidney after en-bloc resection for adrenal carcinoma in a kidney transplant recipient.

CASE REPORT

A 57 year-old male patient had undergone living-donor kidney transplantation for chronic renal failure from hypertension 15 years earlier and had a right adrenal tumor diagnosed on surveillance abdomen-pelvis computerized tomography. Based on 24-hour catecholamine laboratory findings, nonfunctioning tumor was suspected. The planned en-bloc resection of right adrenal gland and right native kidney combining the perirenal tissue and Gerota fascia was performed, because the tumor was suspicious for malignancy and could possibly invade the perirenal tissue or right kidney. On the final pathology, combined adrenal cortical carcinoma and incidental renal cell carcinoma was confirmed. Renal cell carcinoma was papillary, type I, and stage T1N0M0. Adrenal cortical carcinoma was 7.6 × 6.5 cm in size, had marked nuclear atypia, and was grade IV/IV. Mitotic counts were >10 per high-power field, but it had no capsular invasion or vascular invasion, and free resection margin was confirmed. In the preoperative period, he had taken immunosuppressants FK506 and mycophenolate sodium, but after combined carcinomas were confirmed, the regimen of combination of immunosuppressants was changed to sirolimus with low-dose FK506 and half-dose mycophenolate sodium.

Mechanical properties and microstructure of AZ31 Mg alloy containing Ca element fabricated by various rolling speeds

It was reported that the yield strength (YS) of a rolled Mg-3 wt%, Al-1 wt%, Zn-0.3 wt%, Ca alloy reached 340 MPa. The YS value of a rolled Mg-Al-Zn alloy decreases with increasing the rolling speed but that of a rolled Mg-Al-Zn-Ca alloy remains unchanged until the rolling speed of 5 m/min. Static recrystallization behavior in Mg-Al-Zn alloy occurred as a function of rolling speeds; on the other hand, it did not happen in Mg-Al-Zn-Ca alloy. A number of fine precipitates were observed in the grain of the latter alloy, suggesting that they restrain the dislocations from moving during rolling processes and keep the high strength. From the result of boss-forming test, the Mg-Al-Zn-Ca alloy shows more boss-formability than Mg-Al-Zn alloy.

Association of aldehyde dehydrogenase 1 expression and biologically aggressive features in breast cancer

Aldehyde dehydrogenase 1 (ALDH1) has been regarded as a breast cancer stem cell marker. Several studies have reported that ALDH1 expression is associated with poor prognosis in breast cancer. We aimed, therefore, to determine the prognostic value of ALDH1 expression and its association with several biomarkers in breast cancer tissue using immunohistochemistry. Furthermore, we investigated the characteristics of and differences between cellular and stromal expression of ALDH1. We performed tissue microarray (TMA) analysis of 425 breast cancer tissue samples collected during surgery. Immunohistochemical staining was then performed to measure the expression of ALDH1 and other breast cancer biomarkers. Statistical analysis of the relationship between ALDH1 expression and clinicopathologic characteristics was performed for 390 TMA samples. We found that ALDH1 was expressed in 71 cases (18.2%) in the tumor cells and/or stroma. Of these cases, 38 (9.7%) showed ALDH1 expression in tumor cells and 38 (9.7%) showed ALDH1 expression in the stroma. ALDH1 expression was significantly associated with markers of a poor prognosis, such as young age, estrogen receptor negativity, progesterone receptor negativity, a high histological grade, and a high Ki-67 index. However, ALDH1 expression was not associated with p53, transforming growth factor-beta, Gli-1, YKL-40, or sonic hedgehog expression status. With regard to the expression site, the clinical characteristics did not differ between cases of cellular expression and those of stromal expression. However, ALDH1 expression in tumor cells was correlated with hormone receptor status, histological grade, molecular subtype, epidermal growth factor receptor expression status, and cytokeratin 5/6 expression status while stromal expression of ALDH1 was only correlated with hormone receptor status. Overall, these findings suggest that ALDH1 expression in tumor tissue is associated with a biologically aggressive phenotype.

KEYWORDS

ALDH1, biologically aggressive, breast cancer.

Single-molecule views of MutS on mismatched DNA

Base-pair mismatches that occur during DNA replication or recombination can reduce genetic stability or conversely increase genetic diversity. The genetics and biophysical mechanism of mismatch repair (MMR) has been extensively studied since its discovery nearly 50 years ago. MMR is a strand-specific excision-resynthesis reaction that is initiated by MutS homolog (MSH) binding to the mismatched nucleotides. The MSH mismatch-binding signal is then transmitted to the immediate downstream MutL homolog (MLH/PMS) MMR components and ultimately to a distant strand scission site where excision begins. The mechanism of signal transmission has been controversial for decades. We have utilized single molecule Forster Resonance Energy Transfer (smFRET), Fluorescence Tracking (smFT) and Polarization Total Internal Reflection Fluorescence (smP-TIRF) to examine the interactions and dynamic behaviors of single Thermus aquaticus MutS (TaqMutS) particles on mismatched DNA. We determined that TaqMutS forms an incipient clamp to search for a mismatch in ~1 s intervals by 1-dimensional (1D) thermal fluctuation-driven rotational diffusion while in continuous contact with the helical duplex DNA. When MutS encounters a mismatch it lingers for ~3 s to exchange bound ADP for ATP (ADP→ATP exchange). ATP binding by TaqMutS induces an extremely stable clamp conformation (~10 min) that slides off the mismatch and moves along the adjacent duplex DNA driven simply by 1D thermal diffusion. The ATP-bound sliding clamps rotate freely while in discontinuous contact with the DNA. The visualization of a train of MSH proteins suggests that dissociation of ATP-bound sliding clamps from the mismatch permits multiple mismatch-dependent loading events. These direct observations have provided critical clues into understanding the molecular mechanism of MSH proteins during MMR.

The Possibility of TBC1D21 as a Candidate Gene for Teat Numbers in Pigs

Based on a quantitative traits locus (QTL) study using a F₂ intercross between Landrace and Korean native pigs, a significant QTL affecting teat numbers in SSC7 was identified. The strong positional candidate gene, TBC1D21, was selected due to its biological function for epithelial mesenchymal cell development. Sequence analysis revealed six single nucleotide polymorphisms (SNPs) in the TBC1D21 gene. Among these, two SNP markers, one silent mutation (SNP01) for g.13,050A>G and one missense mutation (SNP04) for c.829A>T (S277C), were genotyped and they showed significant associations with teat number traits (p value = 6.38E-05 for SNP01 and p value = 1.06E-07 for SNP04 with total teat numbers). Further functional validation of these SNPs could give valuable information for understanding the teat number variation in pigs.

Loading dynamics of a sliding DNA clamp

Sliding DNA clamps are loaded at a ss/dsDNA junction by a clamp loader that depends on ATP binding for clamp opening. Sequential ATP hydrolysis results in closure of the clamp so that it completely encircles and diffuses on dsDNA. We followed events during loading of an E. coli β clamp in real time by using single-molecule FRET (smFRET). Three successive FRET states were retained for 0.3 s, 0.7 s, and 9 min: Hydrolysis of the first ATP molecule by the γ clamp loader resulted in closure of the clamp in 0.3 s, and after 0.7 s in the closed conformation, the clamp was released to diffuse on the dsDNA for at least 9 min. An additional single-molecule polarization study revealed that the interfacial domain of the clamp rotated in plane by approximately 8° during clamp closure. The single-molecule polarization and FRET studies thus revealed the real-time dynamics of the ATP-hydrolysis-dependent 3D conformational change of the β clamp during loading at a ss/dsDNA junction.

Genome-wide association study identifies quantitative trait loci affecting hematological traits in an F2 intercross between Landrace and Korean native pigs

Changes affecting the status of health and robustness can bring about physiological alterations including hematological parameters in swine. To identify quantitative trait loci (QTL) associated with eight hematological traits (one leukocyte trait, six erythrocyte traits and one platelet trait), we conducted a genome-wide association study using the PorcineSNP60K BeadChip in a resource population derived from an intercross between Landrace and Korean native pigs. A total of 36 740 SNPs from 816 F2 progeny were analyzed for each blood-related trait after filtering for quality control. Data were analyzed by the genome-wide rapid association using mixed model and regression (GRAMMAR) approach. A total of 257 significant SNPs (P < 1.36 × 10(-6) ) on SSC3, 6, 8, 13 and 17 were identified for blood-related traits in this study. Interestingly, the genomic region between 17.9 and 130 Mb on SSC8 was found to be significantly associated with red blood cell, mean corpuscular volume and mean corpuscular hemoglobin. Our results include the identification of five significant SNPs within five candidate genes (KIT, IL15, TXK, ARAP2 and ERG) for hematopoiesis. Further validation of these identified SNPs could give valuable information for understanding the variation of hematological traits in pigs.

Aptamer-based single-molecule imaging of insulin receptors in living cells

We present a single-molecule imaging platform that quantitatively explores the spatiotemporal dynamics of individual insulin receptors in living cells. Modified DNA aptamers that specifically recognize insulin receptors (IRs) with a high affinity were selected through the SELEX process. Using quantum dot-labeled aptamers, we successfully imaged and analyzed the diffusive motions of individual IRs in the plasma membranes of a variety of cell lines (HIR, HEK293, HepG2). We further explored the cholesterol-dependent movement of IRs to address whether cholesterol depletion interferes with IRs and found that cholesterol depletion of the plasma membrane by methyl-β-cyclodextrin reduces the mobility of IRs. The aptamer-based single-molecule imaging of IRs will provide better understanding of insulin signal transduction through the dynamics study of IRs in the plasma membrane.