Developing a Toolbox of Antibodies Validated for Array Tomography-Based Imaging of Brain Synapses

Antibody (Ab)-based imaging techniques rely on reagents whose performance may be application specific. Because commercial antibodies are validated for only a few purposes, users interested in other applications may have to perform extensive in-house antibody testing. Here, we present a novel application-specific proxy screening step to efficiently identify candidate antibodies for array tomography (AT), a serial section volume microscopy technique for high-dimensional quantitative analysis of the cellular proteome. To identify antibodies suitable for AT-based analysis of synapses in mammalian brain, we introduce a heterologous cell-based assay that simulates characteristic features of AT, such as chemical fixation and resin embedding that are likely to influence antibody binding. The assay was included into an initial screening strategy to generate monoclonal antibodies that can be used for AT. This approach simplifies the screening of candidate antibodies and has high predictive value for identifying antibodies suitable for AT analyses. In addition, we have created a comprehensive database of AT-validated antibodies with a neuroscience focus and show that these antibodies have a high likelihood of success for postembedding applications in general, including immunogold electron microscopy. The generation of a large and growing toolbox of AT-compatible antibodies will further enhance the value of this imaging technique.

Developing a Toolbox of Antibodies Validated for Array Tomography-Based Imaging of Brain Synapses

Antibody-based imaging techniques rely on reagents whose performance may be application-specific. Because commercial antibodies are validated for only a few purposes, users interested in other applications may have to perform extensive in-house antibody testing. Here we present a novel application-specific proxy screening step to efficiently identify candidate antibodies for array tomography (AT), a serial section volume microscopy technique for high-dimensional quantitative analysis of the cellular proteome. To identify antibodies suitable for AT-based analysis of synapses in mammalian brain, we introduce a heterologous cell-based assay that simulates characteristic features of AT, such as chemical fixation and resin embedding that are likely to influence antibody binding. The assay was included into an initial screening strategy to generate monoclonal antibodies that can be used for AT. This approach simplifies the screening of candidate antibodies and has high predictive value for identifying antibodies suitable for AT analyses. In addition, we have created a comprehensive database of AT-validated antibodies with a neuroscience focus and show that these antibodies have a high likelihood of success for postembedding applications in general, including immunogold electron microscopy. The generation of a large and growing toolbox of AT-compatible antibodies will further enhance the value of this imaging technique.

High-volume hybridoma sequencing on the NeuroMabSeq platform enables efficient generation of recombinant monoclonal antibodies and scFvs for neuroscience research

The Neuroscience Monoclonal Antibody Sequencing Initiative (NeuroMabSeq) is a concerted effort to determine and make publicly available hybridoma-derived sequences of monoclonal antibodies (mAbs) valuable to neuroscience research. Over 30 years of research and development efforts including those at the UC Davis/NIH NeuroMab Facility have resulted in the generation of a large collection of mouse mAbs validated for neuroscience research. To enhance dissemination and increase the utility of this valuable resource, we applied a high-throughput DNA sequencing approach to determine immunoglobulin heavy and light chain variable domain sequences from source hybridoma cells. The resultant set of sequences was made publicly available as a searchable DNA sequence database (neuromabseq.ucdavis.edu) for sharing, analysis and use in downstream applications. We enhanced the utility, transparency, and reproducibility of the existing mAb collection by using these sequences to develop recombinant mAbs. This enabled their subsequent engineering into alternate forms with distinct utility, including alternate modes of detection in multiplexed labeling, and as miniaturized single chain variable fragments or scFvs. The NeuroMabSeq website and database and the corresponding recombinant antibody collection together serve as a public DNA sequence repository of mouse mAb heavy and light chain variable domain sequences and as an open resource for enhancing dissemination and utility of this valuable collection of validated mAbs.

NeuroMabSeq: high volume acquisition, processing, and curation of hybridoma sequences and their use in generating recombinant monoclonal antibodies and scFvs for neuroscience research

The Neuroscience Monoclonal Antibody Sequencing Initiative (NeuroMabSeq) is a concerted effort to determine and make publicly available hybridoma-derived sequences of monoclonal antibodies (mAbs) valuable to neuroscience research. Over 30 years of research and development efforts including those at the UC Davis/NIH NeuroMab Facility have resulted in the generation of a large collection of mouse mAbs validated for neuroscience research. To enhance dissemination and increase the utility of this valuable resource, we applied a high-throughput DNA sequencing approach to determine immunoglobulin heavy and light chain variable domain sequences from source hybridoma cells. The resultant set of sequences was made publicly available as searchable DNA sequence database ( neuromabseq.ucdavis.edu ) for sharing, analysis and use in downstream applications. We enhanced the utility, transparency, and reproducibility of the existing mAb collection by using these sequences to develop recombinant mAbs. This enabled their subsequent engineering into alternate forms with distinct utility, including alternate modes of detection in multiplexed labeling, and as miniaturized single chain variable fragments or scFvs. The NeuroMabSeq website and database and the corresponding recombinant antibody collection together serve as a public DNA sequence repository of mouse mAb heavy and light chain variable domain sequences and as an open resource for enhancing dissemination and utility of this valuable collection of validated mAbs.

Study on the regulation mechanism of lipopolysaccharide on oxidative stress and lipid metabolism of bovine mammary epithelial cells

The long-term feeding of a high-concentrate diet (the concentrate ratio is greater than 60 %) leads to mammary gland inflammatory response in ruminants and decreased quality in dairy cows and affects the robust development of the dairy industry. The main reason is closely related to elevated lipopolysaccharide (LPS) in the body. In this experiment, a bovine mammary epithelial cell line (MAC-T) was used as a model, and LPS at different concentrations (0 ng/ml, 1 ng/ml, 10 ng/ml, 100 ng/ml, 1000 ng/ml, 10000 ng/ml) was added to the cells. The cell survival rate, oxidative stress indicators, total lipid droplet area, triglyceride content and key genes regulating lipid metabolism were detected by 3-(4,5)-dimethylthiahiazo(-z-y1)-3,5-di-phenytetrazoliumromide (MTT), assay kit, microscope observation and RT-PCR methods to explore the regulatory mechanism of mammary health and milk fat synthesis. The results showed that compared with those of the control group, the survival rates of cells were significantly decreased after 9 h of stimulation with 1000 ng/ml and 10000 ng/ml LPS (P<0.01). The contents of superoxide dismutase (SOD), catalase (CAT) and total antioxidant capacity (T-AOC) in cells were significantly decreased (P<0.05). Compared with that of the control group, the content of malondialdehyde (MDA) in cells was significantly increased (P<0.05) after stimulation with 10000 ng/ml LPS for 9 h. After 9 h of stimulation with 100 ng/ml, 1000 ng/ml and 10000 ng/ml LPS, the total lipid drop area and triglyceride (TG) content of MAC-T cells were significantly decreased (P<0.05). The expression levels of fatty acid synthesis-related genes Acetyl-CoA carboxylase (ACC) and Stearoyl-CoA desaturase 1 (SCD-1) were significantly decreased after 9 h of stimulation with 100 ng/ml, 1000 ng/ml and 10000 ng/ml LPS (P<0.05), while the expression levels of Fatty Acid synthetase (FAS) were significantly decreased after stimulation with 1000 ng/ml and 10000 ng/ml LPS (P<0.05). TG synthesis by the related gene Diacylglycerol acyltransferase-1 (DGAT1) was significantly lower than that of the control group after stimulation with 1000 ng/ml and 10000 ng/ml LPS for 9 h (P<0.05), and Diacylglycerol acyltransferase-2 (DGAT2) also showed a significant decrease after 10000 ng/ml LPS stimulation (P<0.05). In conclusion, adding different concentrations of LPS to MAC-T cells not only led to a decrease in cell activity, resulting in oxidative damage, but also affected fatty acid and TG synthesis, which may ultimately be closely related to the decrease in milk fat synthesis.

Viscoelasticity of 3D actin networks dictated by the mechanochemical characteristics of cross-linkers

In this study, we report a computational investigation on how the mechanochemical characteristics of crosslinking molecules influence the viscoelasticity of three dimensional F-actin networks, an issue of key interest in analyzing the behavior of living cells and biological gels. In particular, it was found that the continuous breakage and rebinding of cross-linkers result in a locally peaked loss modulus in the rheology spectrum of the network, reflecting the fact that maximum energy dissipation is achieved when the driving frequency of the applied oscillating shear becomes comparable to the dissociation/association rate of crosslinking molecules. In addition, we showed that when subjected to constant rate of shear, an actin network can exhibit either strain hardening or softening depending on the ratio between the loading rate and unbinding speed of cross-linkers. A criterion for predicting the transition from softening to hardening was also obtained, in agreement with recent experiments. Finally, significant structural evolution was found to occur in random networks undergoing mechanical "training" (i.e. under a constant applied shear stress over a period of time), eventually leading to a pronounced anisotropic response of the network afterward which again is consistent with experimental observations.

Can deep learning beat numerical weather prediction?

The recent hype about artificial intelligence has sparked renewed interest in applying the successful deep learning (DL) methods for image recognition, speech recognition, robotics, strategic games and other application areas to the field of meteorology. There is some evidence that better weather forecasts can be produced by introducing big data mining and neural networks into the weather prediction workflow. Here, we discuss the question of whether it is possible to completely replace the current numerical weather models and data assimilation systems with DL approaches. This discussion entails a review of state-of-the-art machine learning concepts and their applicability to weather data with its pertinent statistical properties. We think that it is not inconceivable that numerical weather models may one day become obsolete, but a number of fundamental breakthroughs are needed before this goal comes into reach. This article is part of the theme issue 'Machine learning for weather and climate modelling'.

A toolbox of nanobodies developed and validated for use as intrabodies and nanoscale immunolabels in mammalian brain neurons

Nanobodies (nAbs) are small, minimal antibodies that have distinct attributes that make them uniquely suited for certain biomedical research, diagnostic and therapeutic applications. Prominent uses include as intracellular antibodies or intrabodies to bind and deliver cargo to specific proteins and/or subcellular sites within cells, and as nanoscale immunolabels for enhanced tissue penetration and improved spatial imaging resolution. Here, we report the generation and validation of nAbs against a set of proteins prominently expressed at specific subcellular sites in mammalian brain neurons. We describe a novel hierarchical validation pipeline to systematically evaluate nAbs isolated by phage display for effective and specific use as intrabodies and immunolabels in mammalian cells including brain neurons. These nAbs form part of a robust toolbox for targeting proteins with distinct and highly spatially-restricted subcellular localization in mammalian brain neurons, allowing for visualization and/or modulation of structure and function at those sites.

A toolbox of IgG subclass-switched recombinant monoclonal antibodies for enhanced multiplex immunolabeling of brain

Generating recombinant monoclonal antibodies (R-mAbs) from mAb-producing hybridomas offers numerous advantages that increase the effectiveness, reproducibility, and transparent reporting of research. We report here the generation of a novel resource in the form of a library of recombinant R-mAbs validated for neuroscience research. We cloned immunoglobulin G (IgG) variable domains from cryopreserved hybridoma cells and input them into an integrated pipeline for expression and validation of functional R-mAbs. To improve efficiency over standard protocols, we eliminated aberrant Sp2/0-Ag14 hybridoma-derived variable light transcripts using restriction enzyme treatment. Further, we engineered a plasmid backbone that allows for switching of the IgG subclasses without altering target binding specificity to generate R-mAbs useful in simultaneous multiplex labeling experiments not previously possible. The method was also employed to rescue IgG variable sequences and generate functional R-mAbs from a non-viable cryopreserved hybridoma. All R-mAb sequences and plasmids will be archived and disseminated from open source suppliers.

The immune system fights off disease-causing microbes using antibodies: Y-shaped proteins that each bind to a specific foreign molecule. Indeed, these proteins bind so tightly and so specifically that they can pick out a single target in a complex mixture of different molecules. This property also makes them useful in research. For example, neurobiologists can use antibodies to mark target proteins in thin sections of brain tissue. This reveals their position inside brain cells, helping to link the structure of the brain to the roles the different parts of this structure perform.

To use antibodies in this way, scientists need to be able to produce them in large quantities without losing their target specificity. The most common way to do this is with cells called hybridomas. A hybridoma is a hybrid of an antibody-producing immune cell and a cancer cell, and it has properties of both. From the immune cell, it inherits the genes to make a specific type of antibody. From the cancer cell, it inherits the ability to go on dividing forever. In theory, hybridomas should be immortal antibody factories, but they have some limitations. They are expensive to keep alive, hard to transport between labs, and their genes can be unstable. Problems can creep into their genetic code, halting their growth or changing the targets their antibodies recognize. When this happens, scientists can lose vital research tools.

Instead of keeping the immune cells alive, an alternative approach is to make recombinant antibodies. Rather than store the whole cell, this approach just stores the parts of the genes that encode antibody target-specificity. Andrews et al. set out to convert a valuable toolbox of neuroscience antibodies into recombinant form. This involved copying the antibody genes from a large library of preserved hybridoma cells. However, many hybridomas also carry genes that produce non-functional antibodies. A step in the process removed these DNA sequences, ensuring that only working antibodies made it into the final library. Using frozen cells made it possible to recover antibody genes from hybridoma cells that could no longer grow.

The recombinant DNA sequences provide a permanent record of useful antibodies. Not only does this prevent the loss of research tools, it is also much more shareable than living cells. Modifications to the DNA sequences in the library allow for the use of many antibodies at once. This could help when studying the interactions between different molecules in the brain. Toolkits like these could also make it easier to collaborate, and to reproduce data gathered by different researchers around the world.

A Computational Synaptic Antibody Characterization Tool for Array Tomography

Application-specific validation of antibodies is a critical prerequisite for their successful use. Here we introduce an automated framework for characterization and screening of antibodies against synaptic molecules for high-resolution immunofluorescence array tomography (AT). The proposed Synaptic Antibody Characterization Tool (SACT) is designed to provide an automatic, robust, flexible, and efficient tool for antibody characterization at scale. SACT automatically detects puncta of immunofluorescence labeling from candidate antibodies and determines whether a punctum belongs to a synapse. The molecular composition and size of the target synapses expected to contain the antigen is determined by the user, based on biological knowledge. Operationally, the presence of a synapse is defined by the colocalization or adjacency of the candidate antibody punctum to one or more reference antibody puncta. The outputs of SACT are automatically computed measurements such as target synapse density and target specificity ratio that reflect the sensitivity and specificity of immunolabeling with a given candidate antibody. These measurements provide an objective way to characterize and compare the performance of different antibodies against the same target, and can be used to objectively select the antibodies best suited for AT and potentially for other immunolabeling applications.

Electroacupuncture for patients with refractory functional dyspepsia: A randomized controlled trial

BACKGROUND

To test the efficacy of electroacupuncture for patients with refractory functional dyspepsia (FD).

METHODS

A 24-week, 2-arm, single-blind, randomized controlled trial was conducted at three hospitals in China. Patients with refractory FD were randomly assigned to receive 20 sessions of authentic or sham electroacupuncture in a treatment duration of 4 weeks. The primary outcome was complete absence of dyspeptic symptoms at 16 weeks after initiation of acupuncture (week 16). The secondary outcomes included adequate relief of dyspeptic symptoms, Leeds Dyspepsia Questionnaire (LDQ), Nepean Dyspepsia Index (NDI), and adverse events. Intention-to-treat analysis was performed.

KEY RESULTS

Two hundred patients were included, of which 196 (98%) completed follow-up data at week 24. At week 16, 17 (17%) patients in the authentic electroacupuncture group vs 6 (6%) patients in the sham group achieved the primary outcome (P = .014). Sixty-two (62%) patients had adequate relief in the authentic electroacupuncture group, as compared to 22 (22%) in the sham group (P = .001). The scores of LDQ and NDI were significantly improved in both groups at week 16, and patients in the authentic electroacupuncture group have more improvements (LDQ, mean difference, -2.2, 95% confidence interval, -2.3 to -2.1, P < .001; NDI, -7.3, -10.5 to -4.2, P < .001). Results were similar for all the outcomes assessed at week 24. No serious adverse events were reported in both groups.

CONCLUSION

Acupuncture efficaciously improves dyspeptic symptoms in patients with refractory FD.

A Novel Finding: Macrophages Involved in Inflammation Participate in Acute Aortic Dissection Complicated with Acute Lung Injury

BACKGROUND

Little is known about the pathogenesis of acute lung injury (ALI) complicated with acute aortic dissection (AAD).

OBJECTIVE

We aim to investigate the roles of macrophages-derived matrix metalloproteinase 9 (MMP9) in the development of ALI complicated with AAD and factors involved in the recruitment of macrophages.

METHODS

This study included three parts: (i) Determination of serum MMPs, angiotensin II (AngII) and MCP-1 in patients with AAD complicated with ALI or AAD only, non-ruptured chronic aortic aneurysm patients or healthy volunteers using ELISA method. (ii) A novel AAD complicated with ALI model was established by infusing angiotensin II (AngII) to immature rats treated with β-aminopropionitrile monofumarate (BAPN) to identify the potential roles of MMP9 and MCP-1 in AAD complicated with ALI. (iii) Cultured pulmonary microvascular endothelial cell (PMVEC) line was used to investigate how AngII was involved in the release of MCP-1 in rat pulmonary vascular endothelial cells.

RESULTS

Serum MMP9, AngII and MCP-1 were remarkably elevated in patients with AAD complicated with ALI. The MMP9 expressed in pulmonary tissues was derived from macrophages. In the animal model, the release of MMP9 from macrophages finally resulted in ALI, while inhibition of MMP9 and MCP-1 contributed to decreased incidence of AAD complicated with ALI. In vitro experiments indicated that AngII triggered overexpression of MCP-1 in PMVECs by activating NF-κB signaling pathway.

CONCLUSION

AAD complicated with ALI is highly associated with the macrophages infiltrating the pulmonary interstitial tissue and released MMP9 in response to angiotensin II. MCP-1 is closely related to the recruitment of macrophages.

Ventilation inhomogeneity in obstructive lung diseases measured by electrical impedance tomography: a simulation study

Electrical impedance tomography (EIT) has mostly been used in the Intensive Care Unit (ICU) to monitor ventilation distribution but is also promising for the diagnosis in spontaneously breathing patients with obstructive lung diseases. Beside tomographic images, several numerical measures have been proposed to quantitatively assess the lung state. In this study two common measures, the 'Global Inhomogeneity Index' and the 'Coefficient of Variation' were compared regarding their capability to reflect the severity of lung obstruction. A three-dimensional simulation model was used to simulate obstructed lungs, whereby images were reconstructed on a two-dimensional domain. Simulations revealed that minor obstructions are not adequately recognized in the reconstructed images and that obstruction above and below the electrode plane may result in misleading values of inhomogeneity measures. EIT measurements on several electrode planes are necessary to apply these measures in patients with obstructive lung diseases in a promising manner.

Top 50 Landmarks in Sentinel Lymph Node Imaging: A Bibliometric Analysis

Bibliometric analysis can be utilized to identify the most influential literature and track the trajectory of the research development in a given area. The purpose of this study is to summarize the top 50 most-cited landmarks and to examine the recent advances in the field of sentinel lymph node imaging. Web of Science was searched to create a database of all English language scientific journals. This search was then cross referenced with a similar search term query of Scopus to identify articles that may have been missed on the initial search. Articles were ranked by citation counts and screened by two independent reviewers. Citations for the top 50 papers ranged from 2725 to 163 with a median of 240. 10 papers were cited more than 500 times. The articles were published between 1993 - 2009 across 23 journals. Our study identifies intellectual milestones in Sentinel Lymph Node Imaging research, reflecting on the characteristics and quality of the most highly cited literature, and provides a list of the most influential references related to SLNI.

Developing high-quality mouse monoclonal antibodies for neuroscience research - approaches, perspectives and opportunities

High-quality antibodies (Abs) are critical to neuroscience research, as they remain the primary affinity proteomics reagent used to label and capture endogenously expressed protein targets in the nervous system. As in other fields, neuroscientists are frequently confronted with inaccurate and irreproducible Ab-based results and/or reporting. The UC Davis/NIH NeuroMab Facility was created with the mission of addressing the unmet need for high-quality Abs in neuroscience research by applying a unique approach to generate and validate mouse monoclonal antibodies (mAbs) optimized for use against mammalian brain (i.e., NeuroMabs). Here we describe our methodology of multi-step mAb screening focused on identifying mAbs exhibiting efficacy and specificity in labeling mammalian brain samples. We provide examples from NeuroMab screens, and from the subsequent specialized validation of those selected as NeuroMabs. We highlight the particular challenges and considerations of determining specificity for brain immunolabeling. We also describe why our emphasis on extensive validation of large numbers of candidates by immunoblotting and immunohistochemistry against brain samples is essential for identifying those that exhibit efficacy and specificity in those applications to become NeuroMabs. We describe the special attention given to candidates with less common non-IgG1 IgG subclasses that can facilitate simultaneous multiplex labeling with subclass-specific secondary antibodies. We detail our recent use of recombinant cloning of NeuroMabs as a method to archive all NeuroMabs, to unambiguously define NeuroMabs at the DNA sequence level, and to re-engineer IgG1 NeuroMabs to less common IgG subclasses to facilitate their use in multiplex labeling. Finally, we provide suggestions to facilitate Ab development and use, as to design, execution and interpretation of Ab-based neuroscience experiments. Reproducibility in neuroscience research will improve with enhanced Ab validation, unambiguous identification of Abs used in published experiments, and end user proficiency in Ab-based assays.

Compensation for large thorax excursions in EIT imaging

Besides the application of EIT in the intensive care unit it has recently also been used in spontaneously breathing patients suffering from asthma bronchiole, cystic fibrosis (CF) or chronic obstructive pulmonary disease (COPD). In these cases large thorax excursions during deep inspiration, e.g. during lung function testing, lead to artifacts in the reconstructed images. In this paper we introduce a new approach to compensate for image artifacts resulting from excursion induced changes in boundary voltages. It is shown in a simulation study that boundary voltage change due to thorax excursion on a homogeneous model can be used to modify the measured voltages and thus reduce the impact of thorax excursion on the reconstructed images. The applicability of the method on human subjects is demonstrated utilizing a motion-tracking-system. The proposed technique leads to fewer artifacts in the reconstructed images and improves image quality without substantial increase in computational effort, making the approach suitable for real-time imaging of lung ventilation. This might help to establish EIT as a supplemental tool for lung function tests in spontaneously breathing patients to support clinicians in diagnosis and monitoring of disease progression.

Four trace elements in pregnant women and their relationships with adverse pregnancy outcomes

OBJECTIVE

Lack of trace elements during pregnancy is detrimental to maternal and fetal health. Our aim is to study the changes in trace element levels in Chinese pregnant women and their association with adverse pregnancy outcomes.

PATIENTS AND METHODS

1568 cases of Chinese pregnant women in remote areas were collected for a prospective cohort study. Serum copper, zinc, calcium and iron levels were measured at pre-pregnancy, 1st trimester (7w-12w), 2nd trimester (24w-28w) and 3rd trimester (35w-40w).

RESULTS

(1) Serum copper levels was significantly higher after pregnancy than before, calcium and iron levels decreased, but zinc levels did not change significantly. (2) Copper and zinc deficiency in pregnant women was not a common finding, but lack of iron and calcium was frequently encountered; iron deficiency was especially common in the 3rd trimester (42.27%). (3) Serum zinc and iron levels in patients who either had a miscarriage or a preterm delivery were significantly lower than in the control group (p < 0.05). In patients with premature rupture of membranes, serum zinc levels were significantly lower (p < 0.05). In patients with intrauterine growth restriction (IUGR), serum copper, zinc, calcium and iron were significantly lower (p < 0.05).

CONCLUSIONS

Trace elements is closely associated with fetal growth and development during pregnancy. Deficiency can lead to adverse pregnancy outcomes. Therefore, we should have a reasonable diet, replenish trace elements, therefore reducing the occurrence of adverse pregnancy outcomes.

Is microplegia really superior to standard blood cardioplegia? The results from a meta-analysis

Background:

Microplegia (whole blood cardioplegia with reduced volume) retains all the advantages of blood cardioplegia (such as superior oxygen-carrying capacity, better osmotic properties and antioxidant capability, etc.) without the potential disadvantages of hemodilution (such as myocardial edema). We sought to perform a systematic review and meta-analysis to compare microplegia and standard blood cardioplegia on the cardioprotective effects for patients undergoing coronary artery bypass grafting (CABG).

Methods:

MEDLINE, EMBASE and the Cochrane Central Register of Controlled Trials were searched for relevant controlled trials published in English, from their inception up to May 15th, 2013. Data on low output syndrome, spontaneous return to sinus rhythm, volume of cardioplegia and perioperative myocardial infarction were analyzed.

Results:

Five studies, totaling 296 patients, were included out of 77 retrieved citations. The microplegia group used less volume of cardioplegia (WMD, -514.79 ml, 95%CI: -705.37 ml to -324.21 ml) when compared with the standard blood cardioplegia group. There were no statistical differences in the incidence of low output syndrome (RR, 0.95, 95%CI: 0.55 to 1.62), spontaneous return to sinus rhythm (RR, 1.64, 95%CI: 0.61 to 4.41) and perioperative myocardial infarction (RR, 0.62, 95%CI: 0.19 to 2.08).

Conclusions:

Microplegia was associated with less volume of cardioplegia, whereas the incidence of spontaneous return to sinus rhythm and perioperative myocardial infarction were similar, but large controlled randomized trials are still needed to confirm this.

A cultured endophyte community is associated with the plant Clerodendrum inerme and antifungal activity

Fungal endophytes live in the inner tissues of Clerodendrum inerme and may be significant resources for new chemicals in drug discovery. A total of 242 endophytic fungi were recovered from 602 sample segments of C. inerme; 66 were purified. The 66 fungi belonging to 16 taxa and 11 genera (Alternaria, Nigrospora, Bartalinia, Pestalotiopsis, Fusarium, Mycoleptodiscus, Trichoderma, Phomopsis, Diaporthe, Lasiodiplodia, and Curvularia) were identified by morphological characteristics and fungal internal transcribed spacer sequences. The most abundant genera were Alternaria and Lasiodiplodia. Some of the endophytes exhibited tissue specificity. The colonization frequencies of endophytes in the stems were evidently higher than those in the roots and leaves. The crude ethyl acetate extracts were tested against 6 endophytes isolated from C. inerme. Three of 10 (33.3%) endophytes, which were identified as Phomopsis sp, Curvularia sp, and Mycoleptodiscus sp, displayed distinct antifungal activity against ≥3 tested fungi. To our knowledge, this is the first report of an endophytic community associated with C. inerme in China and its antifungal activity in vitro.

Ketamine used as an acesodyne in human breast cancer therapy causes an undesirable side effect, upregulating anti-apoptosis protein Bcl-2 expression

Ketamine is a dissociative anesthetic agent that has been widely used in surgery and for relieving pain in chronic cancer patients. We applied ketamine to breast cancer cell line MDA-MB-231 to detect the effect of treatment and molecular mechanisms involved. We found that ketamine can upregulate the level of anti-apoptosis protein Bcl-2, which promotes breast cancer cell invasion and proliferation. Knockdown of Bcl-2 could inhibit the increase of Bcl-2 and reduce the invasion and proliferation caused by ketamine in human breast cancer cells. Our findings provide new insight into the effects of ketamine in cancer treatment; we suggest that ketamine, which has been widely used in cancer operations and for relieving pain in chronic cancer patients, may be not the best choice because it can worsen the cancer through promotion of anti-apoptosis.

Cell death/proliferation roles for nc886, a non-coding RNA, in the protein kinase R pathway in cholangiocarcinoma

We have recently identified nc886 (pre-miR-886 or vtRNA2-1) as a novel type of non-coding RNA that inhibits activation of protein kinase R (PKR). PKR's pro-apoptotic role through eukaryotic initiation factor 2 α (eIF2α) phosphorylation is well established in the host defense against viral infection. Paradoxically, some cancer patients have elevated PKR activity; however, its cause and consequence are not understood. Initially, we evaluated the expression of nc886, PKR and eIF2α in non-malignant cholangiocyte and cholangiocarcinoma (CCA) cells. nc886 is repressed in CCA cells and this repression is the cause of PKR's activation therein. nc886 alone is necessary and sufficient for suppression of PKR via direct physical interaction. Consistently, artificial suppression of nc886 in cholangiocyte cells activates the canonical PKR/eIF2α cell death pathway, suggesting a potential significance of the nc886 suppression and the consequent PKR activation in eliminating pre-malignant cells during tumorigenesis. In comparison, active PKR in CCA cells does not induce phospho-eIF2α nor apoptosis, but promotes the pro-survival nuclear factor-κB pathway. Thus, PKR has a dual life or death role during tumorigenesis. Similarly to the CCA cell lines, nc886 tends to be decreased but PKR tends to be activated in our clinical samples from CCA patients. Collectively from our data, we propose a tumor surveillance model for nc886's role in the PKR pathway during tumorigenesis.

Temporal separation of aggregation and ubiquitination during early inclusion formation in transgenic mice carrying the Huntington's disease mutation

Abnormal insoluble ubiqitinated protein aggregates are found in the brains of Huntington’s disease (HD) patients and in mice transgenic for the HTT mutation. Here, we describe the earliest stages of visible NII formation in brains of R6/2 mice killed between 2 and 6 weeks of age. We found that huntingtin-positive aggregates formed rapidly (within 24–48 hours) in a spatiotemporal manner similar to that we described previously for ubiquitinated inclusions. However, in most neurons, aggregates are not ubiquitinated when they first form. It has always been assumed that mutant huntingtin is recognised as ‘foreign’ and consequently ubiquitinated and targeted for degradation by the ubiquitin-proteasome system pathway. Our data, however, suggest that aggregation and ubiquitination are separate processes, and that mutant huntingtin fragment is not recognized as ‘abnormal’ by the ubiquitin-proteasome system before aggregation. Rather, mutant Htt appears to aggregate before it is ubiquitinated, and then either aggregated huntingtin is ubiquitinated or ubiquitinated proteins are recruited into aggregates. Our findings have significant implications for the role of the ubiquitin-proteasome system in the formation of aggregates, as they suggest that this system is not involved until after the first aggregates form.

Quantitative assessment of optic nerve head morphology and retinal nerve fibre layer in non-arteritic anterior ischaemic optic neuropathy with optical coherence tomography and confocal scanning laser ophthalmoloscopy

BACKGROUND/AIMS

To compare the optic disc parameters between patients with non-arteritic anterior ischaemic optic neuropathy (NAION) and normal controls, using optical coherence tomography (OCT) and Heidelberg Retinal Tomograph III (HRT), and to evaluate the structure-function relationship in NAION eyes.

METHODS

Both eyes of 22 patients with typical unilateral NAION of > or =6 months' duration and 52 eyes from 52 randomly selected normal subjects underwent Humphrey visual field (HVF) examination and measurement of optic disc and retinal nerve fibre layer thickness (RNFLT).

RESULTS

For the NAION-affected eyes, NAION fellow eyes and normal controls, the ocular magnification-corrected OCT disc areas were respectively 1.849 (SD 0.343) mm(2), 1.809 (0.285) mm(2) and 1.964 (0.386) mm(2); the cup areas were 0.246 (0.187) mm(2), 0.172 (0.180) mm(2) and 0.469 (0.332) mm(2). On HRT, the disc areas were 2.11 (0.38) mm(2), 2.06 (0.40) mm(2) and 2.16 (0.42) mm(2); and the cup areas were 0.28 (0.34) mm(2), 0.25 (0.18) mm(2) and 0.48 (0.32) mm(2). On both OCT and HRT, the cup areas and cup-disc area ratios (CDAR) of both eyes of NAION patients were significantly smaller than controls (p< or =0.01), but the disc areas were not (p> or =0.21). There was a significant correlation between HVF mean deviation and OCT RNFLT (r = 0.44, p = 0.04) but not with HRT RNFLT (p = 0.30) in NAION-affected eyes.

CONCLUSION

NAION patients have smaller optic cups and CDARs in both eyes compared with controls. A larger sample size is necessary to demonstrate if disc size affects the risk of developing NAION. The NAION-affected eyes' OCT RNFLT correlated with HVF mean deviation but the HRT RNFLT did not.

KATP channels depress force by reducing action potential amplitude in mouse EDL and soleus muscle

Although ATP-sensitive K+ (KATP) channel openers depress force, channel blockers have no effect. Furthermore, the effects of channel openers on single action potentials are quite small. These facts raise questions as to whether 1) channel openers reduce force via an activation of KATP channels or via some nonspecific effects and 2) the reduction in force by KATP channels operates by changes in amplitude and duration of the action potential. To answer the first question we tested the hypothesis that pinacidil, a channel opener, does not affect force during fatigue in muscles of Kir6.2-/- mice that have no cell membrane KATP channel activity. When wild-type extensor digitorum longus (EDL) and soleus muscles were stimulated to fatigue with one tetanus per second, pinacidil increased the rate at which force decreased, prevented a rise in resting tension, and improved force recovery. Pinacidil had none of these effects in Kir6.2-/- muscles. To answer the second question, we tested the hypothesis that the effects of KATP channels on membrane excitability are greater during action potential trains than on single action potentials, especially during metabolic stress such as fatigue. During fatigue, M wave areas of control soleus remained constant for 90 s, suggesting no change in action potential amplitude for half of the fatigue period. In the presence of pinacidil, the decrease in M wave areas became significant within 30 s, during which time the rate of fatigue also became significantly faster compared with control muscles. It is therefore concluded that, once activated, KATP channels depress force and that this depression involves a reduction in action potential amplitude.

Expression of mutant huntingtin blocks exocytosis in PC12 cells by depletion of complexin II

Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder caused by an expanded CAG repeat in the HD gene. We reported recently that complexin II, a protein involved in neurotransmitter release, is depleted from both the brains of mice carrying the HD mutation and from the striatum of post mortem HD brains. Here we show that this loss of complexin II is recapitulated in PC12 cells expressing the HD mutation and is accompanied by a dramatic decline in Ca2+-triggered exocytosis of neurotransmitter. Overexpression of complexin II (but not complexin I) rescued exocytosis, demonstrating that the decline in neurotransmitter release is a direct consequence of complexin II depletion. Complexin II depletion in the brain may account for some of the abnormalities in neurotransmission associated with HD.

Kv beta subunit oxidoreductase activity and Kv1 potassium channel trafficking

Voltage-gated Kv1 potassium channels consist of pore-forming alpha subunits and cytoplasmic Kv beta subunits. The latter play diverse roles in modulating the gating, stability, and trafficking of Kv1 channels. The crystallographic structure of the Kv beta2 subunit revealed surprising structural homology with aldo-keto reductases, including a triosephosphate isomerase barrel structure, conservation of key catalytic residues, and a bound NADP(+) cofactor (Gulbis, J. M., Mann, S., and MacKinnon, R. (1999) Cell 90, 943-952). Each Kv1-associated Kv beta subunit (Kv beta 1.1, Kv beta 1.2, Kv beta 2, and Kv beta 3) shares striking amino acid conservation in key catalytic and cofactor binding residues. Here, by a combination of structural modeling and biochemical and cell biological analyses of structure-based mutations, we investigate the potential role for putative Kv beta subunit enzymatic activity in the trafficking of Kv1 channels. We found that all Kv beta subunits promote cell surface expression of coexpressed Kv1.2 alpha subunits in transfected COS-1 cells. Kv beta1.1 and Kv beta 2 point mutants lacking a key catalytic tyrosine residue found in the active site of all aldo-keto reductases have wild-type trafficking characteristics. However, mutations in residues within the NADP(+) binding pocket eliminated effects on Kv1.2 trafficking. In cultured hippocampal neurons, Kv beta subunit coexpression led to axonal targeting of Kv1.2, recapitulating the Kv1.2 localization observed in many brain neurons. Similar to the trafficking results in COS-1 cells, mutations within the cofactor binding pocket reduced axonal targeting of Kv1.2, whereas those in the catalytic tyrosine did not. Together, these data suggest that NADP(+) binding and/or the integrity of the binding pocket structure, but not catalytic activity, of Kv beta subunits is required for intracellular trafficking of Kv1 channel complexes in mammalian cells and for axonal targeting in neurons.

Crescent oligoamides: from acyclic "macrocycles" to folding nanotubes

Oligoarylamides whose backbones are rigidified by intramolecular hydrogen bonds (H-bonds) are found to adopt well-defined conformations in both solution and solid state. Depending on the length of their backbones, these folding oligoamides are crescents, broken macrocycles, or helices. A large (approximately 10 A) interior cavity is associated with the "macrocycles" and helices. The folded conformations are independent of chain length and are found in both nonpolar and polar solvents. This strategy is being extended to the construction of folding acyclic "macrocycles" and nanotubes with larger tubular cavities.

Stable three-center hydrogen bonding in a partially rigidified structure

The three-center hydrogen bond in diaryl amide 1 was examined by IR and 1H NMR spectroscopy, X-ray crystallography, and ab initio calculations. By comparing 1 with its structural isomers 2, 3 and 4, and with its conformational isomers 1a-c, it was found that the two two-center components of the three-center interaction reinforce each other, that is, the enhanced stability of the three-center hydrogen bond is a result of positive cooperativity between the two components. Substituents not involved in hydrogen bonding have little effect on the strength of the two- and three-center hydrogen bonds. To our knowledge, this is the first three-center hydrogen-bonding system that has been shown to exhibit positive cooperativity. Ab initio calculations of the geometries, vibrational modes, and 1H NMR chemical shifts also support the experimental findings. These results have provided a new insight into the three-center intramolecular hydrogen bonding in a partially rigidified structure and have provided a reliable motif for designing stably folded structures.

Sequence Specificity of Hydrogen-Bonded Molecular Duplexes

Hydrogen-bonded molecular duplexes, 1.3 and 1.4, each of which contains a mismatched binding site (acceptor-to-acceptor in 1.3, and donor-to-donor in 1.4), were designed and synthesized based on duplex 1.2. One- and two-dimensional NMR studies demonstrated that, despite their single mismatched binding sites, the backbones of duplexes 1.3 and 1.4 still stayed in register through the formation of the remaining five H-bonds. The backbones of 1.3 and 1.4 adjusted to the presence of the mismatched binding sites by slightly twisting around these sites, which alleviate any head-on repulsive interactions between two H-bond donors (amide O) or between two acceptors (amide H). After 1 equiv of single strand 2, which forms a perfectly matched duplex 1.2 with single strand 1, was added into the solution of either 1.3 or 1.4, only 1.2 and single strand 3 or 4, were detected. Isothermal titration calorimetry (ITC, in chloroform containing 5% DMSO) indicated that duplexes 1.3 and 1.4 were significantly (>40 times) less stable than the corresponding perfectly hydrogen-bonded duplex 1.2. These NMR and ITC results indicate that the pairing of two complementary single strands is not affected by another very similar single strand that contains only one wrong H-bond donor or acceptor, which demonstrates that the self-assembly of this class of H-bonded duplexes is a highly sequence-specific process. The role of these H-bonded duplexes as predictable and programmable molecular recognition units for directing intermolecular interactions has thus been established.

Structural analysis of the binding modes of minor groove ligands comprised of disubstituted benzenes

Two-dimensional homonuclear NMR was used to characterize synthetic DNA minor groove-binding ligands in complexes with oligonucleotides containing three different A-T binding sites. The three ligands studied have a C(2) axis of symmetry and have the same general structural motif of a central para-substituted benzene ring flanked by two meta-substituted rings, giving the molecules a crescent shape. As with other ligands of this shape, specificity seems to arise from a tight fit in the narrow minor groove of the preferred A-T-rich sequences. We found that these ligands slide between binding subsites, behavior attributed to the fact that all of the amide protons in the ligand backbone cannot hydrogen bond to the minor groove simultaneously.

[Classification for two isolates of Microbispora producing immunosuppressants]

Two strains named SIPI-226 and SIPI-207 producing immunosuppressants were isolated from soil samples collected in park of Wuxi city in China. Identification was done by morphological observation, chemical analysis and nucleic acid ribotyping and 16S rRNA sequence. Two strains contain meso-diaminopimelic acid in cell walls, Type PIV phospholipids, a lack of mycolic acids, MK-9(H0, H2, H4) menaquinones and G + C content of 68.3% to 69.4%, and two strains have 97.2% to 98.6% homology in 16S rRNA gene sequences, and the DNA homology by Ribotyping are 53% to 70%, but differ from seven other mesophilic Microbispora rosea strains. It could be concluded that these two strains represented two new subspecies in the genus of Microbispora rosea. We designated the strains as Microbispora rosea subsp. wuxiensis and Microbispora rosea subsp. yuantouzhuensis. The type strains of M. rosea subsp. wuxiensis and M. rosea subsp. yuantouzhuensis are SIPI-226 and SIPI-207, respectively.

Genomic organization and transcriptional regulation of human Apo2/TRAIL gene

Apo2L, or TRAIL, is a type II integral membrane protein belonging to the TNF family which induces apoptotic cell death in a variety of human tumor cells. Apo2L is expressed in many tissues, suggesting that it is nontoxic to normal cells. We found that Apo2L mRNA was induced by interferon (IFN)-alpha and -beta, but not -gamma, in Jurkat cells. To gain a better understanding of the molecular mechanisms that regulate expression of Apo2L, we have characterized the organization of the human Apo2L gene and its promoter region. The Apo2L gene spans approximately 20 kb and is composed of five exons. The 1.2-kb Apo2L promoter region upstream of the translation initiation codon was cloned, its transcription start site defined, and several putative transcription factor binding sites identified. Luciferase reporter constructs were transfected into Jurkat cells and shown to be induced by IFNs. Deletion analysis indicates that the Apo2L promoter region between nucleotides 126 and 33 upstream of the transcriptional start site controls the expression of the Apo2L gene following IFN-beta treatment.

A K(ATP) channel deficiency affects resting tension, not contractile force, during fatigue in skeletal muscle

The objective of this study was to determine how an ATP-sensitive K(+) (K(ATP)) channel deficiency affects the contractile and fatigue characteristics of extensor digitorum longus (EDL) and soleus muscle of 2- to 3-mo-old and 1-yr-old mice. K(ATP) channel-deficient mice were obtained by disrupting the Kir6.2 gene that encodes for the protein forming the pore of the channel. At 2-3 mo of age, the force-frequency curve, the twitch, and the tetanic force of EDL and soleus muscle of K(ATP) channel-deficient mice were not significantly different from those in wild-type mice. However, the tetanic force and maximum rate of force development decreased with aging to a greater extent in EDL and soleus muscle of K(ATP) channel-deficient mice (24-40%) than in muscle of wild-type mice (7-17%). During fatigue, the K(ATP) channel deficiency had no effect on the decrease in tetanic force in EDL and soleus muscle, whereas it caused a significantly greater increase in resting tension when compared with muscle of wild-type mice. The recovery of tetanic force after fatigue was not affected by the deficiency in 2- to 3-mo-old mice, whereas in 1-yr-old mice, force recovery was significantly less in muscle of K(ATP) channel-deficient than wild-type mice. It is suggested that the major function of the K(ATP) channel during fatigue is to reduce the development of a resting tension and not to contribute to the decrease in force. It is also suggested that the K(ATP) channel plays an important role in protecting muscle function in older mice.

Apo2 ligand/TNF-related apoptosis-inducing ligand and death receptor 5 mediate the apoptotic signaling induced by ionizing radiation in leukemic cells

Ionizing radiation is a major tool for cancer treatment. The response of eukaryotic cells to ionizing radiation includes apoptosis, a process which requires activation of multiple genes. We sought to determine whether radiation-induced gene expression plays a role in radiation-induced apoptosis. We found Apo2 ligand (Apo2L, also called TRAIL) mRNA induction following gamma-irradiation of Jurkat, MOLT-4, CEM, and PBMC, all human T lineage-derived cells. Increased Apo2L protein levels were found in MOLT-4 and Jurkat cells. Radiation also activated the Apo2L death receptor (DR)5 (also called Apo2, TRAIL-R2, or KILLER) in MOLT-4 cells, which harbor a wild-type p53. We isolated 1152 bp of 5' flanking region of the Apo2L gene and a shorter fragment of 716 bp, both of which showed promoter activity driving the expression of a luciferase reporter gene; however, the response to radiation in MOLT-4 cells was lost when only 430 bp of 5' proximal flanking sequence was maintained. Exogenous Apo2L induced phosphatidylserine exposure on cell membranes, caspase 8 and caspase 3 activation, key markers of apoptosis, confirming that the Apo2L/DR5 pathway is functional in these cells. Bid, a Bcl-2 family protein also known to contribute to receptor-mediated apoptosis, was also activated. To determine whether Apo2L and DR5 were critical for radiation signaling to apoptosis, we stably expressed a dominant negative DR5delta-receptor in Jurkat cells. Cell survival was significantly augmented, indicating that increased Apo2L expression contributed to radiation-induced apoptosis. Clonogenic assays demonstrated that purified, recombinant soluble Apo2L enhanced the lethality of low, therapeutic doses (1-2 Gy) of gamma-irradiation. These data suggest that production of Apo2L may cooperate synergistically with the cytotoxic effect of radiation, and that combinations of Apo2L and radiation may become a powerful tool in clinical therapy.