Optimal reference genes for real-time quantitative PCR and the expression of sigma factors in Acidithiobacillus caldus under various conditions

AIMS

Acidithiobacillus caldus is an important sulphur-oxidizing bacterium that plays crucial roles in the bioleaching industry. This study aims to analyse the optimal reference gene for real-time quantitative PCR (RT-qPCR) under different conditions and investigate the transcription levels of the sigma factor genes in the stress response.

METHODS AND RESULTS

We selected six housekeeping genes and analysed them via RT-qPCR using two energy resources, under four stress conditions. Three statistical approaches BestKeeper, geNorm, and NormFinder were utilized to determine transcription stability of these reference genes. The gapdH gene was the best internal control gene using elemental sulphur as an energy resource and under heat stress, map was the best internal control gene under pH and osmotic stress, era was the best internal control gene for the K₂ S₄ O₆ energy resource, and rpoC was the best internal control gene under Cu²⁺ stress. Furthermore, the expressional levels of 11 sigma factors were analysed by RT-qPCR in the stress response.

CONCLUSIONS

Stable internal control genes for RT-qPCR analysis of A. caldus were determined, and the expression patterns of sigma factor genes of A. caldus were investigated.

SIGNIFICANCE AND IMPACT OF THE STUDY

The identification of the optimal reference gene and analysis of transcription levels of sigma factors in A. caldus can provide clues for reference gene selection and the study of sigma factor function.

Optical rogue waves in coupled fiber Raman lasers

For coupled linear cavity-random fiber Raman lasers, for the first time, to the best of our knowledge, we demonstrate a new mechanism of emergence of the random pulses, with the anomalous statistics satisfying optical rogue waves' criteria experimentally. The rogue waves appear as a result of the coupling of two Raman cascades, namely, a linear cavity laser with a wavelength of 1.55 µm and a random laser with a wavelength nearly 1.67 µm, along with coupling of the orthogonal states of polarization (SOPs). The coherent coupling of SOPs causes localization of the trajectories in the vicinity of these states, whereas polarization instability drives escape taking the form of chaotic oscillations. Antiphase dynamics in two cascades result in the suppression of low amplitude chaotic oscillations and enable the anomalous spikes, satisfying rogue waves criteria.

Combination of pegylated interferon-alpha and nucleos(t)ide analogue treatment enhances the activity of natural killer cells in nucleos(t)ide analogue experienced chronic hepatitis B patients

A combination of pegylated interferon-alpha (peg-IFN-α) and nucleos(t)ides analogue (NA) therapy can effectively reduce hepatitis B surface antigen (HBsAg), especially in NA-experienced chronic hepatitis B (CHB) patients. However, the immune mechanism of this therapy is unclear. Forty NA-experienced CHB patients were enrolled into this study. The frequencies of peripheral blood natural killer (NK) cells, dendritic cells (DCs), CD4⁺ T cells, CD8⁺ T cells, T helper (Th) cells, regulatory T cells (T_reg ), B cells and follicular T helper (Tfh) cells were evaluated by flow cytometry. Seven of the 40 patients converted to peg-IFN-α combined with NA treatment, while the other 33 continued to NA therapy. The decrease in HBsAg was more pronounced in the combination treatment group, and only patients receiving combination treatment achieved HBsAg loss. The frequency and absolute number of CD56^bright NK cells in the combination treatment group increased significantly compared with the NA treatment group, whereas the CD56^dim NK cells were decreased. In the NA treatment group, the proportions of CD4⁺ T_N , CD8⁺ T_N , CD19⁺ B and cytotoxic T lymphocyte antigen-4 (CTLA-4)⁺ CD4⁺ T cells were increased, while the proportions of CD4⁺ T_EM , CD8⁺ T_EM , CD25⁺ CD4⁺ T_reg , CD25^high CD4⁺ T_reg , CD127^low CD25⁺ T_reg , programmed cell death 1 (PD-1)⁺ CD4⁺ T, PD-1⁺ CD8⁺ T, CTLA-4⁺ CD8⁺ T, CCR4⁺ CD25⁺ T_reg and CCR4⁺ CD25^high T_reg cells were decreased after therapy. For NA-experienced CHB patients who achieved low HBsAg levels, combination treatment is more likely to result in HBsAg decline and HBsAg clearance by increasing the activity of CD56^bright NK cells.

Combined therapy of infusion of DC from rats with higher expression of IDO and CD40L on rejection post heart transplantation

OBJECTIVE

Indoleamine 2, 3-dioxygenase (IDO) can inhibit rejection of graft via inducing T cell apoptosis. CD40L monoclonal antibody (mAb) inhibits T cell activation. However, the effects of the combination of infusion of dendritic cell (DC) from IDO over-expressed donor mice and CD40L mAb on the treatment of graft rejection after heart transplantation have not been reported.

MATERIALS AND METHODS

Allogeneic heart transplantation mouse model was established. Recipient mice were divided into three groups, including control group, IDO group (in which DC donors received adenoviral vector of IDO) and combined therapy group (which received both IDO over-expressed DC infusion and CD40L mAb injection post transplantation). Survival time and cardiac function were observed, with IDO expression being quantified. Flow cytometry (FCM) was used to analyze T cell apoptosis, while enzyme linked immunosorbent assay (ELISA) was adopted to test the levels of interferon-γ (IFN-γ), interleukin-2 (IL-2), interleukin-10 (IL-10) and interleukin-6 (IL-6).

RESULTS

IDO expression was significantly elevated in both IDO and combined therapy groups, with enhanced T cell apoptosis compared to control group (p < 0.05). Both groups had better survival time and cardiac functions compared to control group, along with increased IL-10/IL-6 expression and suppressed INF-γ and IL-2 expression (p < 0.05). However, combined therapy had a better efficiency compared to IDO group (p < 0.05).

CONCLUSIONS

Combined therapy of high IDO expressed mouse DC perfusion with CD40L mAb can elongate the survival time of recipient heart and inhibit rejection reaction via facilitating T cell apoptosis. Meanwhile, combined therapy could also regulate the expression of some immune suppressant factors and mediate the Th1/Th2 cytokine balance.

Decreased A20 expression on circulating CD56bright NK cells contributes to a worse disease status in patients with ankylosing spondylitis

A20, a pivotal anti-inflammatory protein, preserves immune homeostasis and regulates prolonged inflammation. A previous study has shown that A20 expression levels are down-regulated in peripheral blood mononuclear cells (PBMCs) from patients with ankylosing spondylitis (AS). However, the precise role of A20 in reducing autoimmune disorders needs to be further elucidated. In this study, A20 expression was found to be preferentially reduced on circulating CD56^bright natural killer (NK) cells in patients with AS, and its level was negatively correlated with that of proinflammatory cytokines. Further investigation demonstrated that A20 reduces interferon (IFN)-γ and tumour necrosis factor (TNF)-α production in CD56^bright NK cells after stimulation with monokines or phorbol myristate acetate (PMA)/ionomycin(P/I). Furthermore, CD56^bright NK cells isolated from AS patients promote TNF-α secretion by autologous monocytes, and increasing the A20 expression level partially attenuates this process. More importantly, decreased A20 expression on circulating CD56^bright NK cells is associated with worse disease status in patients with AS. Our findings reveal that A20 participates in the pathogenesis of AS by negatively regulating CD56^bright NK cells and that its reduced expression contributes to a worsened disease status in patients with AS.

Targeted next-generation sequencing and parental genotyping in sporadic Chinese Han deaf patients

The interpretation of the targeted next-generation sequencing (NGS) results can be challenging for variants identified in the sporadic deaf patients. In this study, we performed targeted NGS of 143 deafness-associated genes in 44 sporadic deaf patients and use parental genotyping to test whether the candidate pathogenic variants complied with recessive or de novo pattern. Of 29 recessive candidate variants with minor allele frequencies (MAFs) less than 0.005, 3 pairs of apparent compound heterozygous variants were inherited from the same parental allele, ruling out their pathogenic roles. In addition, non-segregation of an OTOA p.Gln293Arg variant led to the discovery of a genomic microdeletion of OTOA on the opposite allele by copy number variation analysis. Overall, 13 pairs of recessive candidate variants were deemed causative in 13 patients. Of the 28 dominant candidate variants with MAFs less than 0.0005, none occurred de novo, suggesting that they were not disease causing. Our results revealed that targeted NGS in sporadic deaf patients may generate a significant false-positive rate. Parental genotyping is a simple but effective step toward minimizing the false-positive results. Our study also showed that de novo variants in dominant deafness genes may not be a common cause for sporadic deafness.

The effectiveness of anterior cervical decompression and fusion for the relief of dizziness in patients with cervical spondylosis: a multicentre prospective cohort study

AIMS

Cervical spondylosis is often accompanied by dizziness. It has recently been shown that the ingrowth of Ruffini corpuscles into diseased cervical discs may be related to cervicogenic dizziness. In order to evaluate whether cervicogenic dizziness stems from the diseased cervical disc, we performed a prospective cohort study to assess the effectiveness of anterior cervical discectomy and fusion on the relief of dizziness.

PATIENTS AND METHODS

Of 145 patients with cervical spondylosis and dizziness, 116 underwent anterior cervical decompression and fusion and 29 underwent conservative treatment. All were followed up for one year. The primary outcomes were measures of the intensity and frequency of dizziness. Secondary outcomes were changes in the modified Japanese Orthopaedic Association (mJOA) score and a visual analogue scale score for neck pain.

RESULTS

There were significantly lower scores for the intensity and frequency of dizziness in the surgical group compared with the conservative group at different time points during the one-year follow-up period (p = 0.001). There was a significant improvement in mJOA scores in the surgical group.

CONCLUSION

This study indicates that anterior cervical surgery can relieve dizziness in patients with cervical spondylosis and that dizziness is an accompanying manifestation of cervical spondylosis. Cite this article: Bone Joint J 2018;100-B:81-7.

Bax/Bak activation in the absence of Bid, Bim, Puma, and p53

How BH3-only proteins activate Bax/Bak, the two gateway proteins of the mitochondria-dependent apoptotic pathway, remains incompletely understood. Although all pro-apoptotic BH3-only proteins are known to bind/neutralize the anti-apoptotic Bcl-2 proteins, the three most potent ones, Bid (tBid), Bim, and Puma, possess an additional activity of directly activating Bax/Bak in vitro. This latter activity has been proposed to be responsible for triggering Bax/Bak activation following apoptotic stimulation. To test this hypothesis, we generated Bid^−/−Bim^−/−Puma^−/− (TKO), TKO/Bax^−/−/Bak^−/− (PentaKO), and PentaKO/Mcl-1^−/− (HexaKO) HCT116 cells through gene editing. Surprisingly, although the TKO cells were resistant to several apoptotic stimuli, robust apoptosis was induced upon the simultaneous inactivation of Bcl-xL and Mcl-1, two anti-apoptotic Bcl-2 proteins known to suppress Bax/Bak activation and activity. Importantly, such apoptotic activity was completely abolished in the PentaKO cells. In addition, ABT-737, a BH3 mimetic that inhibits Bcl-xL/Bcl-w/Bcl-2, induced Bax activation in HexaKO cells reconstituted with endogenous level of GFP-Bax. Further, by generating TKO/p53^−/− (QKO) cells, we demonstrated that p53, a tumor suppressor postulated to directly activate Bax, is not required for Bid/Bim/Puma-independent Bax/Bak activation. Together, these results strongly suggest that the direct activation activities of Bid (tBid), Bim, Puma, and p53 are not essential for activating Bax/Bak once the anti-apoptotic Bcl-2 proteins are neutralized.

Strategy of STAT3β cell-specific expression in macrophages exhibits antitumor effects on mouse breast cancer

Recent studies underscore the importance of crosstalk between tumor-associated macrophages (TAMs) and tumor cells in cancer progression and metastasis. In our study, AdCD68STAT3β, a recombinant adenovirus containing a STAT3β gene driven by CD68 macrophage-specific promoter, was used to suppress STAT3 and the downstream signaling pathways in TAMs. The results showed that STAT3β gene under the control of CD68 macrophage-specific promoter was only expressed in macrophages, which significantly inhibited the motility and invasion of breast cancer cells when co-cultured with 4T1 cells. Moreover, cell-specific STAT3β expression in TAMs extended survival of tumor-bearing mice and suppressed breast tumor growth, angiogenesis and metastasis, by regulating the crosstalk between tumor cells and TAMs. Therefore, our study provided a novel strategy for the antitumor effects of STAT3β.

Advances in non-peptidomimetic HIV protease inhibitors

HIV protease plays a crucial role in the viral life cycle. It can cleave a series of heptamers in the viral Gag and GagPol precursor proteins to generate mature infectious virus particles. Successful inhibition of the protease will prevent this maturation step and hence block the spreading of HIV. However, the rapid emergence of drug resistance makes it urgent to develop new HIV protease inhibitors to combat the global disease. Besides, poor oral bioavailability, unacceptable side effects, high treatment cost and pill burden also trouble the application of HIV protease inhibitors. In such situations, non-peptidomimetic HIV protease inhibitors have drawn an increasing interest as a potential therapeutic option due to their small molecular weight, favorable bioavailability, high stability in vivo, low resistance and cost of production. In this review, we present the recent advances in non-peptidomimetic HIV protease inhibitors. Their design strategies, biological activities, resistance profiles, as well as clinical application will also be discussed.

Mapping shape quantitative trait loci using a radius-centroid-contour model

As the consequence of complex interactions between different parts of an organ, shape can be used as a predictor of structural-functional relationships implicated in changing environments. Despite such importance, however, it is no surprise that little is known about the genetic detail involved in shape variation, because no approach is currently available for mapping quantitative trait loci (QTLs) that control shape. Here, we address this problem by developing a statistical model that integrates the principle of shape analysis into a mixture-model-based likelihood formulated for QTL mapping. One state-of-the-art approach for shape analysis is to identify and analyze the polar coordinates of anatomical landmarks on a shape measured in terms of radii from the centroid to the contour at regular intervals. A procrustes analysis is used to align shapes to filter out position, scale and rotation effects on shape variation. To the end, the accurate and quantitative representation of a shape is produced with aligned radius-centroid-contour (RCC) curves, that is, a function of radial angle at the centroid. The high dimensionality of the RCC data, crucial for a comprehensive description of the geometric feature of a shape, is reduced by principal component (PC) analysis, and the resulting PC axes are treated as phenotypic traits, allowing specific QTLs for global and local shape variability to be mapped, respectively. The usefulness and utilization of the new model for shape mapping in practice are validated by analyzing a mapping data collected from a natural population of poplar, Populus szechuanica var tibetica, and identifying several QTLs for leaf shape in this species. The model provides a powerful tool to compute which genes determine biological shape in plants, animals and humans.

Effects of degradable MG-ND-ZN-ZR alloy on osteoblastic cell function

This study aimed to investigate the effects of a novel patented Mg-3Nd-0.2Zn-0.4Zr (weight %, JDBM) alloy on osteoblastic cell function, as these cells play an important role in bone repair and remodeling. The associated effects of the JDBM alloy on osteoblastic cell function involving cell adhesion, cell proliferation, and mineralization were investigated using scanning electron microscopy (SEM), MTT assay and ambramycin staining, respectively. At the same time, the in vitro degradation behavior of the JDBM alloy in cell culture medium was evaluated by the weight-loss method and SEM. Pure magnesium was used as control. The results showed that osteoblastic cells cultured on JDBM alloy samples manifested better cell adhesion, improved cell proliferation and increased mineralization ability, compared with cells seeded on pure magnesium samples. Our data indicate that the JDBM alloy has excellent bioactivity, improving the cell function of osteoblastic cells seeded on it.

Assessing the potential of candidate DNA barcodes for identifying non-flowering seed plants

In plants, matK and rbcL have been selected as core barcodes by the Consortium for the Barcode of Life (CBOL) Plant Working Group (PWG), and ITS/ITS2 and psbA-trnH were suggested as supplementary loci. Yet, research on DNA barcoding of non-flowering seed plants has been less extensive, and the evaluation of DNA barcodes in this division has been limited thus far. Here, we evaluated seven markers (psbA-trnH, matK, rbcL, rpoB, rpoC1, ITS and ITS2) from non-flowering seed plants. The usefulness of each region was assessed using four criteria: the success rate of PCR amplification, the differential intra- and inter-specific divergences, the DNA barcoding gap and the ability to discriminate species. Among the seven loci tested, ITS2 produced the best results in the barcoding of non-flowering seed plants. In addition, we compared the abilities of the five most-recommended markers (psbA-trnH, matK, rbcL, ITS and ITS2) to identify additional species using a large database of gymnosperms from GenBank. ITS2 remained effective for species identification in a wide range of non-flowering seed plants: for the 1531 samples from 608 species of 80 diverse genera, ITS2 correctly authenticated 66% of them at the species level. In conclusion, the ITS2 region can serve as a useful barcode to discriminate non-flowering seed plants, and this study will contribute valuable information for the barcoding of plant species.

Comparison of micafungin and voriconazole in the treatment of invasive fungal infections in kidney transplant recipients

WHAT IS KNOWN AND OBJECTIVE

Invasive fungal infections are a major threat to renal transplant recipients. Micafungin and voriconazole are two useful antifungal agents for treating such infections. Our objective is to evaluate the comparative efficacy and safety of micafungin and voriconazole in the initial treatment of such infections.

METHODS

In this prospective, multicentre, open-labelled, randomized, controlled trial, renal transplant recipients with invasive fungal infections were assigned to receive either micafungin or voriconazole. The enrolled subjects received a kidney transplant between March 2008 and March 2010 at one of the two transplant centres in Henan Province, China. The efficacy and adverse effects of the two treatments were compared.

RESULTS AND DISCUSSION

The clinical trial enrolled 65 patients, of whom 31 were treated with micafungin, and 34 with voriconazole. The rates of microbiological evidence of infection in the micafungin and voriconazole groups were 64.5% and 70.5%, respectively, whereas the rates of Candida as the major cultured fungus were 80.0% and 75.0%, respectively. Complicated bacterial infection rates in the two treatment groups were 38.7% and 32.4%, respectively, whereas complicated CMV viral infection occurred at a rate of 19.2% and 23.5%, respectively. Fungal infection within one to 3 months after transplant was 83.6% (26/31) and 85.3% (29/34) in the micafungin and voriconazole groups, respectively. There was no significant difference between the two groups in terms of efficacy, survival beyond 10 days and discontinuation of treatment because of lack of efficacy (P > 0.05). Mortality rates in the micafungin and voriconazole groups were 9.7% (3/31) and 12.1% (4/33), respectively. Rates of adverse effects in the two groups were 41.9% and 51.6% (P > 0.05), respectively.

WHAT IS NEW AND CONCLUSIONS

This is the first comparison of micafungin and voriconazole in renal transplant patients. Our study shows that the effectiveness of micafungin was similar to that of voriconazole in such patients.

Xanthohumol, a prenylated chalcone derived from hops, suppresses cancer cell invasion through inhibiting the expression of CXCR4 chemokine receptor

Cancer metastasis is the main cause of death (90%), and only recently we have gained some insight into the mechanisms by which metastatic cells arise from primary tumors and target to specific organs. Cysteine X Cysteine (CXC) chemokine receptor 4 (CXCR4), initially linked with leukocyte trafficking, is overexpressed in various tumors and mediates homing of tumor cells to distant sites expressing its cognate ligand CXCL12. Therefore, identification of CXCR4 inhibitors has great potential to abrogate tumor metastasis. In this study, we demonstrated that xanthohumol (XN), a prenylflavonoid derived from the female flowers of the hops plant (Humulus lupulus. L), suppressed CXCR4 expression in various cancer cell types in a concentration- and time-dependent manner. Both proteasome and lysosomal inhibitors had no effect to prevent the XN-induced downregulation of CXCR4, suggesting that the inhibitory effect of XN was not due to proteolytic degradation but occurred at the transcriptional level. Electrophoretic mobility shift assay and chromatin immunoprecipitation assay further confirmed that XN could block endogenous activation of nuclear factor kappa B, a key transcription factor regulates the expression of CXCR4 in cancer cells. Consistent with the above molecular basis, XN abolished cell invasion induced by CXCL12 in both breast and colon cancer cells. Interestingly, although co-exist in hops, XN is the only isoform that exhibited the inhibitory effect on the expression of CXCR4 compared with other isomers, isoxanthohumol and 8-prenylnaringenin. Together, our results suggested that XN, as a novel inhibitor of CXCR4, could be a promising therapeutic agent contributed to cancer treatment.

Complementary deoxyribonucleic acid cloning of avian G0/G1 switch gene 2, and its expression and association with production traits in chicken

As a member of the G0/G1 switch genes, G0/G1 switch gene 2 (G0S2) is related to many regulatory processes in the human and mouse. For example, it interacts directly with adipose triglyceride lipase to active its triglyceride hydrolysis activities. In this study, G0S2 gene cDNA of the chicken (522 bp), zebra finch (420 bp), sparrow (417 bp), pigeon (417 bp), and Bengalese finch (416 bp) were cloned, and each of them was encoded as a protein of 99 amino acids. The expression of G0S2 mRNA was determined by real-time reverse-transcription PCR analysis in 20 tested tissues of 21- and 91-d-old chickens. The highest mRNA level was found in abdominal fat and subcutaneous fat in both stages. Considerable G0S2 mRNA was also observed in chicken heart and muscle tissues. Expression of the chicken G0S2 gene varied at different stages and sexes. The abundance of G0S2 mRNA on d 21 was far higher than that on d 91. The abundance in female chickens was higher than that in males at both stages. In the coding region, we found 4 SNP, among which only G197A led to a change in the amino acids (Arg66Gln); the rest were synonymous substitutions. Association analysis showed that both G102A and G255A were significantly associated with head width (P < 0.05) and were highly significantly associated with leg muscle color (P < 0.01). The G102A was significantly associated with shank diameter at 63 d (P < 0.05). The SNP G197A was significantly associated with shank diameter at 49 d; CP content of leg muscle; total weights of the heart, liver, gizzard, and glandular stomach; and small intestine length (P < 0.05). In conclusion, much higher G0S2 mRNA was detected in both male and female chickens at 21 d of age than at 91 d of age, and 3 SNP (G102A, G197, and G255A) were associated with chicken production traits.

ERIC-PCR-based strain-specific detection of phenol-degrading bacteria in activated sludge of wastewater treatment systems

AIMS

To evaluate the use of Enterobacterial Repetitive Intergenic Consensus PCR (ERIC-PCR)-derived probes and primers to specifically detect bacterial strains in an activated sludge microbial community.

METHODS AND RESULTS

ERIC-PCR was performed on two phenol-degrading bacterial strains, Arthrobacter nicotianae P1-7 and Klebsiella sp. P8-14. Their amplicons were DIG labelled for use as probes and then hybridized with ERIC-PCR fingerprints. The results showed the distinct band patterns for both bacterial strains. Strain-specific PCR primers were designed based on the sequences of ERIC-PCR bands. The DNA of each of these strains was successfully detected from its mixture with activated sludge DNA, either by using their respective ERIC-PCR-based probes for hybridization or by using species-specific primers for amplification, with higher sensitivity by latter method.

CONCLUSIONS

Two phenol-degrading bacterial strains were identified from a mixture of activated sludge by using ERIC-PCR-based methods.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study demonstrated that the bacteria, which have important functions in complex wastewater treatment microbial communities, could be specifically detected by using ERIC-PCR fingerprint-based hybridization or amplification.

Diffractive grating structure for coherent light source production

A diffractive structure of cavities is designed to produce resonances at very high frequencies. This type of cavity structure may be useful for producing controllable coherent synchrotron radiation by microbunching the particle beam.