Guidelines for the use and interpretation of assays for monitoring autophagy

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

Acute inhibition of GSK causes mitochondrial remodeling

Recent data have shown that cardioprotection can result in the import of specific proteins into the mitochondria in a process that involves heat shock protein 90 (HSP90) and is blocked by geldanamycin (GD), a HSP90 inhibitor. To test the hypothesis that an alteration in mitochondrial import is a more widespread feature of cardioprotection, in this study, we used a broad-based proteomics approach to investigate changes in the mitochondrial proteome following cardioprotection induced by inhibition of glycogen synthase kinase (GSK)-3. Mitochondria were isolated from control hearts, and hearts were perfused with the GSK inhibitor SB 216763 (SB) for 15 min before isolation of mitochondria. Mitochondrial extracts from control and SB-perfused hearts were labeled with isotope tags for relative and absolute quantification (iTRAQ), and differences in mitochondrial protein levels were determined by mass spectrometry. To test for the role of HSP90-mediated protein import, hearts were perfused in the presence and absence of GD for 15 min before perfusion with SB followed by mitochondrial isolation and iTRAQ labeling. We confirmed that treatment with GD blocked the protection afforded by SB treatment in a protocol of 20 min of ischemia and 40 min of reperfusion. We found 16 proteins that showed an apparent increase in the mitochondrial fraction following SB treatment. GD treatment significantly blocked the SB-mediated increase in mitochondrial association for five of these proteins, which included annexin A6, vinculin, and pyruvate kinase. We also found that SB treatment resulted in a decrease in mitochondrial content of eight proteins, of which all but two are established mitochondrial proteins. To confirm a role for mitochondrial import versus a change in protein synthesis and/or degradation, we measured changes in these proteins in whole cell extracts. Taken together, these data show that SB leads to a remodeling of the mitochondrial proteome that is partially GD sensitive.

Effects of electroacupuncture pretreatment on inflammatory response and acute kidney injury in endotoxaemic rats

This study investigated the effect of electroacupuncture pretreatment on the lipopolysaccharide (LPS)-induced inflammatory response and on acute kidney injury in adult male pathogen-free Wistar rats. Rats received electroacupuncture at the Zusanli (ST36) and Neiguan (PC6) acupoints, or electrical stimulation at sham points, for 30 min before stimulation with either 5 mg/kg LPS intravenously or normal saline. Plasma cytokines, plasma nitrite, renal inducible nitric oxide synthase (iNOS) and nuclear factor κB (NF-κB) activity were assessed 240 min after LPS or normal saline injection. Blood urea nitrogen (BUN), creatinine (Cr) and histopathological score for renal tubular damage were also measured. Electroacupuncture pretreatment significantly decreased LPS-induced plasma tumour necrosis factor-α and interleukin (IL)-1β, increased plasma IL-10, and decreased plasma nitrite, renal iNOS and NF-κB activity. It also significantly decreased LPS-induced BUN, Cr and the renal histopathological score. These findings suggest that electroacupuncture pretreatment at the ST36 and PC6 acupoints attenuated the LPS-induced inflammatory response and mitigated acute kidney injury.

Surfactant protein D inhibits lipopolysaccharide-induced monocyte chemoattractant protein-1 expression in human renal tubular epithelial cells: implication for tubulointerstitial fibrosis

Surfactant protein D (SP-D), a member of the C-type lectin (collectin) protein family, plays a critical role in innate host defence against various microbial pathogens and in the modulation of inflammatory responses in the lung. However, little is known about its expression and biological function in the kidney. In this work, we studied SP-D expression in human kidney and cultured human renal proximal tubular epithelial cells (HK-2), and examined the effect of SP-D on proinflammatory cytokine production after lipopolysaccharide (LPS) stimulus. We observed the expression of both SP-D mRNA and protein in human kidney and in-vitro HK-2 cells by immunohistochemistry, Western blot analysis, reverse transcription-polymerase chain reaction (RT-PCR) and real-time PCR. To explore the potential role of SP-D in the pathogenesis of tubulointerstitial fibrosis in kidney infection, we examined the production of monocyte chemoattractant protein-1 (MCP-1) in HK-2 cells after LPS treatment. Results showed that the level of MCP-1 in the conditioned medium increased significantly when HK-2 cells were cultured with LPS (>0·1 µg/ml) for 8 h. Of interest, LPS treatment inhibited SP-D expression in HK-2 cells. Furthermore, over-expression of SP-D reduced significantly the LPS-induced expression of MCP-1 in transfected cells. These findings suggest that SP-D in the kidney functions as an anti-inflammatory factor in renal tubular epithelial cells and may modulate tubulointerstitial fibrosis in kidney.

High segregation distortion in maize B73 x teosinte crosses

Two genetic linkage maps of cultivated maize inbred lines and teosinte species were constructed. One population comprised 81 F(2) individuals derived from a cross between maize inbred line B73 and Zea mays ssp parviglumis, while the second consisted of 63 backcross individuals from a cross of maize inbred line B73 with Z. mays ssp diploperennis. In the B73 x Z. mays ssp parviglumis F(2) population, 172 simple sequence repeat (SSR) markers were mapped to 10 chromosomes, which covered 2210.8 cM. In the B73 x Z. mays ssp diploperennis backcross population, 258 SSR markers were mapped to 10 chromosomes, covering 1357.7 cM. Comparison of the two maps revealed that the total map length of Z. mays ssp diploperennis covers 1357.7 cM, which is about 61.4% of that of Z. mays ssp parviglumis (2210.8 cM). Extensive segregation distortion regions were found on chromosomes 1, 2, 3, 5, 6, 7, and 10 in the B73 x Z. mays ssp parviglumis F(2) population and on chromosomes 1-5 and 8-10 in the B73 x Z. mays ssp parviglumis backcross population. Segregation distortion analysis confirmed that the segregation distortion ratio in the interspecific population B73 x Z. mays ssp diploperennis was higher than in B73 x Z. mays ssp parviglumis. We found that the recombination distances are highly variable in these genetic crosses between cultivated and wild species of maize.

Digital microfluidic operations on micro-electrode dot array architecture

As digital microfluidics-based biochips find more applications, their complexity is expected to increase significantly owing to the trend of multiple and concurrent assays on the chip. There is a pressing need to deliver a top-down design methodology that the biochip designer can leverage the same level of computer-aided design support as the semi-conductor industry now does. Moreover, as microelectronics fabrication technology is scaling up and integrated device performance is improving, it is expected that these microfluidic biochips will be integrated with microelectronic components in next-generation system-on-chip designs. This study presents the analysis and experiments of digital microfluidic operations on a novel electrowetting-on-dielectric-based 'micro-electrode dot array architecture' that fosters a development path for hierarchical top-down design approach for digital microfluidics. The proposed architecture allows dynamic configurations and activations of identical basic microfluidic unit called 'micro-electrode cells' to design microfluidic components, layouts, routing, microfluidic operations and applications of the biochip hierarchically. Fundamental microfluidic operations have been successfully performed by the architecture. In addition, this novel architecture demonstrates a number of advantages and flexibilities over the conventional digital microfluidics in performing advanced microfluidic operations.

Photonic generation of tunable microwave signal using Brillouin fiber laser

A simple approach to generate two bands of tunable microwave signal is proposed and demonstrated. In this scheme, two single-mode fibers with optimized Brillouin frequency shift spacing have been chosen as the scattering medium in two cascaded ring cavities. Two bands of tunable microwave signal from 390 to 453 MHz and 10.863 to 11.076 GHz can be obtained through adjusting the temperature of the fiber and the pump wavelength. The tunable frequency range can be further expanded by using a temperature controller with a wider adjustment range. The generated microwave signal exhibits high stability on frequency.

Reutilization of immobilized fungus Rhizopus sp. LG04 to reduce toxic chromate

AIMS

Most of the researches investigating immobilized fungi in chromate [Cr(VI)] bioremediation have used dead cells to adsorb Cr(VI). Therefore, the aim was to identify a Cr(VI)-reducing fungus with the ability of reducing the toxic Cr(VI) into the much less toxic Cr(III) and to apply the immobilized living fungus in continual reduction of Cr(VI).

METHODS AND RESULTS

Cr(VI) reduction occurred using both free fungi and immobilized living Rhizopus sp. LG04. The Cr(VI) bioreduction by the free fungi was achieved mainly by bioreduction coupled with a small amount of biosorption on the cell surfaces. LG04 spores immobilized with 3% polyvinyl alcohol and 3% sodium alginate produced the most stable and efficient biobeads. When the LG04 biobeads were washed and transferred into fresh medium containing 42 mg l(-1) of Cr(VI), the biobeads could be reused to reduce Cr(VI) for more than 30 cycles during an 82-day operation period. Interestingly, as the cycles increased, the time required for complete reduction stabilized at approximately 2·5 days, which was faster than that obtained using the free fungi (4·5 days). The pH value of the solution decreased from 6·60 ± 0·10 to 3·85 ± 0·15 after each reduction cycle, which may be because the metabolic products of the fungus changed the environmental pH or because there was an accumulation of the organo-Cr(III) complex.

CONCLUSIONS

The results indicate that using the immobilized living fungus for the removal of Cr(VI) has the advantages in being stable, long-term treatment, easy to re-use and less biomass leakage.

SIGNIFICANCE AND IMPACT OF THE STUDY

To our knowledge, this study reports the first successful use of immobilized living Rhizopus for the repeated reduction of Cr(VI).

Discovery- and target-based protein quantification using iTRAQ and pulsed Q collision induced dissociation (PQD)

Pulsed Q collision-induced dissociation (PQD) was developed in part to facilitate detection of low-mass reporter ions using labeling reagents (e.g. iTRAQ) on LTQ platforms. It has generally been recognized that the scan speed and sensitivity of an LTQ are superior than those of an Orbitrap using the higher-energy collisional dissociation (HCD). However, the use of PQD in quantitative proteomics is limited, primarily due to the meager reproducibility of reporter ion ratios. Optimizations of PQD for iTRAQ quantification using LTQ have been reported, but a universally applicable strategy for quantifying the less abundant proteins has not been fully established. Adjustments of the AGC target, μscan, or scan speed offer only incremental improvements in reproducibility. From our experience, however, satisfactory coefficients of variation (CVs) of reporter ion ratios were difficult to achieve using the discovery-based approach. As an alternative, we implemented a target-based approach that obviates data dependency to allow repetitive data acquisitions across chromatographic peaks. Such a strategy generates enough data points for more reliable quantification. Using cAMP treatment in S49 cell lysates and this target-based approach, we were able to validate differentially expressed proteins, which were initially identified as potential candidates using the discovery-based PQD. The target-based strategy also yielded results comparable to those obtained from HCD in an Orbitrap. Our findings should aid LTQ users who desire to explore iTRAQ quantitative proteomics but have limited access to the more costly Orbitrap or other instruments.

Identified hadron compositions in p+p and Au+Au collisions at high transverse momenta at √S(NN)=200 GeV

We report transverse momentum (p(T)≤15  GeV/c) spectra of π(±), K(±), p, p[over ¯], K(S)(0), and ρ(0) at midrapidity in p+p and Au+Au collisions at √S(NN)=200  GeV. Perturbative QCD calculations are consistent with π(±) spectra in p+p collisions but do not reproduce K and p(p[over ¯]) spectra. The observed decreasing antiparticle-to-particle ratios with increasing p(T) provide experimental evidence for varying quark and gluon jet contributions to high-p(T) hadron yields. The relative hadron abundances in Au+Au at p(T)≳8  GeV/c are measured to be similar to the p+p results, despite the expected Casimir effect for parton energy loss.

Strangeness enhancement in Cu-Cu and Au-Au collisions at √S(NN)=200 GeV

We report new STAR measurements of midrapidity yields for the Λ, Λ[over ¯], K(S)(0), Ξ(-), Ξ[over ¯](+), Ω(-), Ω[over ¯](+) particles in Cu+Cu collisions at √S(NN)==200  GeV, and midrapidity yields for the Λ, Λ[over ¯], K(S)(0) particles in Au+Au at √S(NN)==200  GeV. We show that, at a given number of participating nucleons, the production of strange hadrons is higher in Cu+Cu collisions than in Au+Au collisions at the same center-of-mass energy. We find that aspects of the enhancement factors for all particles can be described by a parametrization based on the fraction of participants that undergo multiple collisions.

Hollow CoFe₂O₄ nanospheres as a high capacity anode material for lithium ion batteries

Hollow structured CoFe₂O₄ nanospheres were synthesized by a hydrothermal method. The uniform hollow nanosphere architecture of the as-prepared CoFe₂O₄ has been confirmed by field emission scanning electron microscopy and transmission electron microscopy analysis, which give an outer diameter of 200-300 nm and a wall thickness of about 100 nm. CoFe₂O₄ nanospheres exhibited a high reversible capacity of 1266 mA h g⁻¹ with an excellent capacity retention of 93.6% over 50 cycles and an improved rate capability. CoFe₂O₄ could be a promising high capacity anode material for lithium ion batteries.

Development and preliminary application of an indirect ELISA for detecting antibodies against Avian Influenza Virus

Fragment of 759 bp DNA spanning the Matrix 1 (M1) gene of Avian Influenza Virus (AIV) was inserted into an expression vector pET28c to construct a recombinant plasmid pET28c-M1. The pET28c-M1 plasmid was transformed into the Escherichia coli BL21 (DE3) competent cell to produce a recombinant strain E. coli 21 (DE3). After being induced by Isopropyl-b-D-galactopyranoside (IPTG), E. coli 21 (DE3) expressed a 28-kDa fusion protein at a high level. This protein can bind anti-AIV (H5N1) positive serum by Western-blot analysis. After being denatured, renatured, and purified by Ni(2+)-column, the fusion protein was used as an antigen to develop Matrix 1 Enzyme-Linked Immunosorbent Assay (M1-ELISA) for detecting antibodies against AIV from chicken serum. We found that this indirect M1-ELISA was sensitive for differentiating antisera against AIV and antisera against other six kinds of avian viruses apart from AIV and this method is more sensitive than Hemagglutination Inhibition (HI) test. When compared with HI test and ELISA (IDEXX) in evaluating 581 serum samples from field vaccinated chickens, this assay showed 93.3% agreement ratio with the HI test, as well as 96.0% agreement ratio with ELISA (IDEXX). In a preliminary application, the assay successfully detected 19 AIVs from 51 nonvaccinated chicken lungs. It concludes that an indirect ELISA was successfully developed for detecting AIV. The assay is specific and sensitive. The application will greatly contribute to the long-term prevention and control of avian influenza in China.

219 ISOLATION AND CHARACTERIZATION OF DOMESTIC CAT SPERMATOGONIAL CELLS

Spermatogonial stem cells (SSC) have the capacity for self-renewal and the potential of producing progenitor spermatogonia that will differentiate into spermatozoa. SSC transplantation may be a valuable alternative for the propagation of genetically important males and preservation of endangered wild felids, as recently demonstrated by the production of ocelot spermatozoa after the xeno-transplantation of a mixed germ cell population into the testis of a domestic cat (Silva et al. 2011 J. Androl.). SSC are in low numbers in the testis and have been isolated in different mammalian species by using specific cell surface markers; however, the expression of SSC-surface markers in feline species has not been characterised. In the present study, testes of domestic cats were obtained from veterinary clinics. The selected testes (n = 4) ranged in size from 1.3 to 2.0 cm in length. To obtain a suspension of a mixed population of spermatogonial cells, seminiferous tubules were enzymatically dissociated using two digestion steps followed by dual filtration through 100-μm and 40-μm nylon mesh filters and a final separation over a 5-layer Percoll™ density gradient (35, 30, 27.5, 25 and 20%). Spermatogonial cells were morphologically identified by their characteristic large round nucleus with a homogenous appearance in the bands formed at the 30%, 27.5% and 25% layers. The mean number of cells/testis collected was ∼13 × 106 ± 12.2, with an overall percentage of live cells of 97%. After isolation, cells were fixed with 4% PFA, blocked overnight and stained with primary antibodies specific for SSC-surface markers (CD49f, CD9, C-Kit, GFRα1, GPR125 and Thy-1) and pluripotent stage-specific embryonic antigen markers (SSEA-1 and SSEA-4). Fluorescence microscopy showed a positive expression of GFRα1, GPR125 and C-Kit, but not for CD49f, CD9, or Thy-1. It also revealed that a low number of cells were positive for SSEA-1 and SSEA-4. For further characterisation, molecular detection of the pluripotent gene Oct-4 and the germ cell-specific genes BOLL, DAZL and VASA was performed in germ cells isolated from one testis of four individuals. For RT-qPCR, the Cells-to-cDNA™ II kit (Ambion) was used to produce cDNA from an aliquot of ∼30 000 cells directly after isolation. RT-qPCR showed that none had detectable levels of Oct-4 within the range of the standard. Three of the four testes expressed all three germ cell-specific genes, BOLL, DAZL and VASA, while only VASA was detected in the remaining testis. These results suggest that cat SSCs and spermatogonial cells express some of the SSC markers tested. However, the positive expression of SSEA-1 and SSEA-4 in a low number of cells further supports the stem cell-like state of cat SSCs and that these markers can be used in dual staining for purifying cat SSCs from a mixed germ cell population by fluorescence-activated cell sorting.

Refractive index sensor using microfiber-based Mach-Zehnder interferometer

A simple and robust refractive index (RI) sensor based on a Mach-Zehnder interferometer has been demonstrated. A section of optical microfiber drawn from silica fiber is employed as the sensing arm. Because of the evanescent field, a slight change of the ambient RI will lead to the variation of the microfiber propagation constant, which will further change the optical length. In order to compensate the variation of the optical length difference, a tunable optical delay line (ODL) is inserted into the other arm. By measuring the delay of the ODL, the ambient RI can be simply demodulated. A high RI sensitivity of about 7159  μm/refractive index unit is achieved at microfiber diameter of 2.0 μm.