SGN nerve filaments develop synapses with IHCs earlier than with OHCs in C57BL/6 mouse inner ear

OBJECTIVE

To explore the connections between hair cells and spiral ganglion neurons (SGNs) during the development of the C57BL/6 mouse inner ear.

MATERIALS AND METHODS

The specimens of C57BL/6 mouse inner ear, from E15 (embryo day 15) to adult mouse, were collected; immunohistochemistry was employed to explore the frozen sections of specimens.

RESULTS

The development of cochlea starts sequentially from the basal turn to the apex turn. Morphological development of SGNs occurs mainly from E16 to P12 (postnatal day 12). Hair cells appear from E18 to P12, and inner hair cells (IHCs) develop earlier than outer hair cells (OHCs). The connections between hair cells and SGNs begin to develop during E18-P1, morphologically resemble mature synapses during P8-P12, and completely mature in adult mice.

CONCLUSIONS

The genesis of auditory ribbon synapse occurs from E18 to P1. Synchronized with the development of SGNs and hair cells, the functional filaments remain connected to hair cells, while the spare ones get disconnected from the surface of hair cells. Connections between SGN nerve filaments and IHCs occur earlier than those between SGN nerve filaments and OHCs.

The delimitation of intestine segments of koi carp (Cyprinus carpio var. koi) based on histological features

In this study, the delimitation of intestine segments of koi carp (Cyprinus carpio var. koi) was conducted using a histological approach with the measurements of height of mucosa folds (HF), width of mucosa folds (WF), thickness of muscularis (TM) and cross-sectional area (CSA). According to the change trends for these four parameters, the intestine of the koi carp was divided into anterior intestine, middle intestine and posterior intestine. The locations of the three intestine segments were defined, and their ratios along the entire intestine were accounted for 23.84 ± 1.18%, 46.77 ± 2.29% and 29.39 ± 1.65%, respectively. The anterior intestine had a significantly higher HF, compared with the middle (p < .01) or posterior intestines (p < .01). The muscularis became thin gradually from the anterior intestine to posterior part. TM was significantly different among the anterior, middle and posterior intestines (p < .01). The anterior intestine had a significantly higher CSA, compared with the middle (p < .01) and posterior intestines (p < .01), and the latter two segments had similar CSA values (p > .05). The procedure of the delimitation of the koi carp intestine segments can offer useful information for future studies on other fish species. The presented results are meaningful for studies on differential functions of the different intestine segments in fish.

Effects of supplementation of sea buckthorn press cake on mycelium growth and polysaccharides of Inonotus obliquus in submerged cultivation

AIMS

Investigation of the influence of cultivation time and sea buckthorn press cake (Hippophaë rhamnoides) dosage on mycelium yield of Inonotus obliquus in submerged cultivation and on the yield, monomer composition, and macromolecular properties of the exopolysaccharides (EPS) from culture media and intracellular polysaccharides (IPS) extracted from mycelia.

METHODS AND RESULTS

Supplementation at 5 g l^-1 combined with cultivation time of 250 h granted highest yield increase in mycelia (by 122%). The supplementation reduced extraction yield and decreased the molecular weight of the main IPS population. The supplementation increased production and molecular weight of EPS. The relative content of arabinose and rhamnose in EPS positively correlated with dosage of the press cake. The press cake supplementation increased the content of galacturonic acid in IPS, but not in EPS.

CONCLUSION

Sea buckthorn press cake is a food industry fibrous side stream with high oil content. It increases the cultivation yield of Inonotus obliquus mycelium and influences the produced polysaccharides.

SIGNIFICANCE AND IMPACT OF THE STUDY

Mycelium is a resource of bioactive polysaccharides, attracting the interest of nutraceutical companies. Sea buckthorn press cake is a promising supplement for increasing mycelium production. The utilization of this agricultural side stream would therefore favour circular economy.

Spatial variation of the soil bacterial community in major apple producing regions of China

AIMS

In China, apple production areas are largely from the coastal to inland areas and across varied climate zones. However, the relationship among soil micro-organisms, environmental factors and fruit quality has not been clearly confirmed in orchards. Here we attempted to identify the variation of soil bacteria in the main apple producing regions and reveal the relationship among climatic factor, soil properties, soil bacterial community and fruit quality.

METHODS AND RESULTS

Sixty soil samples were collected from six main apple producing areas in China. We examined the soil bacteria using bacterial 16S rRNA gene amplicon profiling. The results show that the soil bacterial diversity of apple orchards varied from the Bohai Bay Region to the Loess Plateau Region. Proteobacteria, Acidobacteria and Actinobacteria were the predominant taxa at the phylum level for all six areas. In the Bohai Bay and the Loess Plateau region, which are the two largest apple producing areas, Proteobacteria and Actinobacteria had the highest relative abundance, respectively. Furthermore, soil bacterial diversity showed positive correlation with the mean annual temperature (MAT), soil organic matter (SOM) and pH. Excluding a direct effect on the apple fruit quality, MAT exerted an indirect influence through soil SOM and pH to alter the relative abundance of dominant taxa and shift the bacterial diversity, which affects the apple fruit titratable acids and soluble solids.

CONCLUSIONS

Geographic variables underlie apple orchard soil bacterial communities vary according to spatial scale. Environmental factors exert an indirect effect on apple fruit quality via shaping soil bacterial community.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides a list of bacteria associated with environmental factors and the ecological attributes of their interactions in apple orchards, which will improve our ability to promote soil bacterial functional capabilities in order to reduce the fertilizer input and enhance the fruit quality.

Influence of mesenchymal stem cells on respiratory distress syndrome in newborn swines via the JAK-STAT signaling pathway

OBJECTIVE

Acute respiratory distress syndrome (ARDS) threatens humans' health worldwide, causing huge labor and economic cost investment. This study aims to explore whether mesenchymal stem cells (MSCs) affect RDS in newborn swines via the Janus kinase-signal transducers and activators of transcription (JAK-STAT) signaling pathway by the establishment of the model of the disease.

MATERIALS AND METHODS

The phosphorylation of the JAK-STAT signal transduction proteins was first detected via Western blotting to verify the regulatory effect of MSCs on RDS in newborn swines through the JAK-STAT signaling pathway. Then, the Reverse Transcription-Polymerase Chain Reaction (RT-PCR) was utilized to analyze the influences of the injection of MSCs into the blood of newborn model RDS swines on inflammatory factors in vivo. To further demonstrate the signal transduction function put forwarded, the RT-PCR and enzyme-linked immunosorbent assay (ELISA) were adopted to analyze the influences of the JAK-STAT signaling pathway inhibitor on the expression of the signature proteins of RDS in newborn swines and the changes in the inflammatory factors.

RESULTS

MSCs induced the phosphorylation of JAK and STAT, and they activated the JAK-STAT signal transduction of RDS in newborn swines. Compared with those in normal saline group, the interleukin (IL)-2, IL-6, IL-8, and tumor necrosis factor-α (TNF-α) expression levels in MSC group were increased, namely, MSCs substantially promoted their expression levels (p<0.05), but those of IL-10 and IL-13 were significantly decreased (p<0.05).

CONCLUSIONS

The inhibitor of the JAK-STAT signaling pathway can suppress the therapeutic effect of MSCs on RDS in newborn swines.

Differentially expressed proteins in the intestine of Cynoglossus semilaevis Günther following a Shewanella algae challenge

Fish intestine is an important constituent of the mucosal immune system. The gut and gut-associated lymphoid tissue construct a local immune environment. A Shewanella algae strain was previously reported to be a pathogen causing ascitic disease accompanied with intestinal inflammation in Cynoglossus semilaevis. This study aimed to investigate the intestine immune response in C. semilaevis to S. algae infection at the protein level. Two-dimensional electrophoresis coupled with mass spectrometry proteomics was utilized to compare protein expression in the intestines from normal and S. algae-infected C. semilaevis. A total of 70 differentially expressed proteins (DEPs), consisting of 16 upregulated and 54 downregulated proteins, were identified in the intestine tissue of C. Semilaevis. These protein expression changes were further validated using western blot analysis and quantitative real-time PCR. Gene ontology enrichment analysis showed that these 70 DEPs could be assigned across three categories: "cellular components", "molecular function", and "biological process". Forty-one DEPs (six up-regulated and 35 down-regulated proteins) related to metabolic processes were identified. In addition, 20 DEPs (eight up-regulated and 12 down-regulated proteins) related to stress and immune responses were identified. A protein-protein interaction network generated by the STRING (Search Tool for the Retrieval of Interacting Genes/protein) revealed that 30 DEPs interacted with one another to form an integrated network. Among them, 29 DEPs were related to stress, immune, and metabolism processes. In the network, some of the immune related proteins (C9, FGB, KNG1, apolipoprotein A-IV-like, and PDIA3) were up-regulated and most DEPs involved in metabolism processes were down-regulated. These results indicate that the immune defense response of the intestine was activated and the intestinal function associated with metabolism processes was disturbed. This study provides valuable information for further research into the functions of these DEPs in fish.

PERSPECTIVE: Critical Cooling and Warming Rates as a Function of CPA Concentration

Cryoprotective agents (CPAs) are routinely applied in cryopreservation protocols to achieve the vitrified state thereby avoiding the damaging effects of ice crystals. Once the CPA has been added, the system needs to cool at a rate ≥ critical cooling rate (CCR) to avoid ice crystallization and successfully enter the vitrified state. Subsequently, upon warming the system needs to meet or exceed a critical warming rate (CWR), often one to two orders of magnitude higher than the CCR, to avoid ice formation and return the system to physiological temperatures for use. Many experimental and theoretical studies have been published on CCRs and CWRs, and correlation for these rates as a function of concentration has been explored for some single component CPAs, but not the CPA cocktails which are commonly used in tissue and organ cryopreservation. In this paper, we summarize the available data of CCRs and CWRs for a variety of CPAs, and suggest a convenient mathematical expression for CCR and CWR that can guide general use for cryoprotective protocol, but also highlights the critical need for further study on CPA cocktails and tissue systems in which CPAs may behave differently and/or may not be fully equilibrated to the loaded CPA.

Ultrafast temporal-spatial dynamics of amorphous-to-crystalline phase transition in Ge2Sb2Te5 thin film triggered by multiple femtosecond laser pulses irradiation

Studies have shown that the crystallization phase state of Ge₂Sb₂Te₅ (GST) can be reversibly modulated by femtosecond (fs) laser multiple pulses, which have excellent applications in reconfigurable multi-level operation fields. In this study, the temporal-spatial crystalline evolution dynamics of amorphous GST film is investigated during two fs laser pulses excitation through a pump-probe shadowgraph imaging technique. A quasi-amorphous phase state, which is different from that in the initial as-deposited amorphous GST, is emerged through the first fs laser pulse excitation with a pulse energy lower than crystallization threshold. The experimental results reveal that a crystallization enhancement effect can be induced through the second pulse excitation based on this quasi-amorphous surface structure. The stimulative cluster generated in the quasi-amorphous reduces the amorphous-to-crystalline phase transition threshold for the second fs laser pulse irradiation. The spatially-resolved phase-transition threshold extension effect in a horizontal direction is proposed with the increasing pulse number to summarize the mechanism of the crystallization enhancement effect. The specific-grain-appearance (coarse grains and fine grains representing different phase transition approach) distributed area induced by single and double fs laser pulses irradiation are experimentally demonstrated corresponding to threshold extension theory.

Sensitivity of SWIFT spectroscopy

SWIFT spectroscopy (Shifted Wave Interference Fourier Transform Spectroscopy) is a coherent beatnote technique that can be used to measure the temporal profiles of periodic optical signals. While it has been essential in understanding the physics of various mid-infrared and terahertz frequency combs, its ultimate limits have not been discussed. We show that the envelope of a SWIFTS interferogram is physically meaningful and is directly related to autocorrelation. We derive analytical expressions for the SWIFTS signals of two prototypical cases-chirped pulses from a mode-locked laser and a frequency-modulated comb-and derive scaling laws for the noise of these measurements, showing how it can be mitigated. Finally, we confirm this analysis by performing the first SWIFTS measurements of near-infrared pulses from femtosecond lasers, establishing the validity of the technique for highly-dispersed sub-picojoule pulses.

Apple rootstocks with different phosphorus efficiency exhibit alterations in rhizosphere bacterial structure

AIMS

The purpose of this study was to select phosphorus-efficient apple rootstocks under phosphorus deficiency and to reveal the effects of different apple rootstocks on the rhizosphere bacterial community.

METHODS AND RESULTS

We used 83 hybrid lines of Malus robusta Rehd. × Malling 9 (M.9) to investigate their physiological traits and the phosphorus deficiency phenotypes of leaves in response to phosphorus deficiency (0·1 mmol l^-1 PO₄ ^3- ). All the plants were cultivated in pots in the greenhouse and watered using drip irrigation. In accordance with the results of investigation, we selected the phosphorus-efficient hybrid lines (PE) and the phosphorus-inefficient hybrid lines (PI) to research their root morphology and root hairs (RH). In addition, we used Illumina MiSeq sequencing to determine the bacterial community of the rhizosphere from different rootstocks. The results showed that the PE plants had better growth characteristics and stronger root plasticity than that of the PI plants, and phosphorus deficiency can stimulate the RH growth of PE plants. There was no significant difference in the rhizosphere bacterial diversity, but we found that the bacterial community structure was significantly different at the genus levels; in addition, 89 genera were found to have significant differences between PE and PI plants, especially Bacillus. The PE rhizosphere had more abundant Bacillus compared to the PI. High positive Pearson correlations with the phosphorus concentration in the plantlets of apple rootstocks were detected for the bacterial genera Bacillus (r: 0·776).

CONCLUSIONS

The phosphorus-efficient apple rootstocks adapted to phosphorus deficiency by shaping the root morphology. Notably, different apple rootstocks showed alteration of the microbes in rhizosphere.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study can provide the materials for exploring the mechanism of apple rootstock phosphorus absorption. In accordance with the different bacterial community compositions, we can develop the inoculants to promote nutrient uptake.

HIV-1 genotype is independently associated with immunodeficiency progression among Chinese men who have sex with men: an observational cohort study

OBJECTIVES

HIV-1 genetic diversity is increasing among men who have sex with men (MSM) in China, but the association of HIV-1 genotype with disease progression remains to be elucidated.

METHODS

We collected data in an observational longitudinal cohort study of 860 HIV-1-infected MSM in Guangzhou, China between January 2008 and March 2017. Kaplan-Meier analysis and Cox proportional hazard model were used to predict the time from HIV-1 diagnosis to immunodeficiency progression (CD4 cell count < 200 cells/μl) as well as adjusted hazard ratio (aHR).

RESULTS

CRF01_AE and HIV-1 subtype B infection were associated with higher percentage of patients progressed to immunodeficiency and higher incidence of immunodeficiency than infection with CRF07_BC or CRF55_01B. Compared with CRF07_BC, the time from HIV-1 diagnosis to immunodeficiency were different among the major HIV-1 genotypes, which ranked as follows, in descending order: CRF07_BC (7.03 years) > CRF55_01B (5.71 years, P = 0.014; aHR 3.752, P = 0.0923) > CRF01_AE (5.18 years, P < 0.001; aHR 4.733, P = 0.0152). HIV-1 genotype, viral load and baseline CD4 T-cell count were three independent variables associated with disease progression.

CONCLUSIONS

Our results confirm differential rates of immunodeficiency progression as a function of HIV-1 genotype. The impact of HIV-1 genotype on HIV epidemics, patient management and prevention should be further investigated.

Role of Adult Tissue-Derived Pluripotent Stem Cells in Bone Regeneration

Background

Bone marrow-derived mononuclear cells (BM-MNC) consist of a heterogeneous mix of mesenchymal stem cells (MSC), hematopoietic progenitor cells (HPC), endothelial progenitor cells (EPC), monocytes, lymphocytes and pluripotent stem cells. Whereas the importance of MSC and EPC has been well documented in bone healing and regeneration studies, the role of pluripotent stem cells is still poorly understood. In the present study we evaluated if and how Very Small Embryonic Like cells (VSEL), isolated from rat BM-MNC, contribute to bone healing.

Methods

Large bone defects were made in the femurs of 38 Sprague Dawley female rats and treated with β-TCP scaffold granules seeded with male VSEL; BM-MNC, VSEL-depleted BM-MNC or scaffold alone, and bone healing was evaluated at 8 weeks post-surgery.

Results

Bone healing was significantly increased in defects treated with VSEL and BM-MNC, compared to defects treated with VSEL-depleted BM-MNC. Donor cells were detected in new bone tissue, in all the defects treated with cells, and in fibrous tissue only in defects treated with VSEL-depleted BM-MNC. The number of CD68+ cells was the highest in the VSEL-depleted group, whereas the number of TRAP positive cells was the lowest in this group.

Conclusions

Based on the results, we can conclude that VSEL play a role in BM-MNC induced bone formation. In our rat femur defect model, in defects treated with VSEL-depleted BM-MNC, osteoclastogenesis and bone formation were decreased, and foreign body reaction was increased.

Isolation, Identification and Characteristics of Aeromonas veronii From Diseased Crucian Carp (Carassius auratus gibelio)

Aeromonas species often cause disease in farmed fish. In the present study, dominant bacteria were isolated from diseased crucian carp (Carassius auratus gibelio). Based on this, a bacterial isolate was tentatively named CFJY-623. This isolate was identified as Aeromonas veronii based on analysis of its morphological, physiological, and biochemical features, as well as 16S rRNA and gyrB gene sequences. Six virulence genes related to pathogenicity including aerolysin, cytotonic enterotoxins, elastase, glycerophospholipid: cholesterol acyltransferase, lipase, and serine protease were identified in this A. veronii isolate. The median lethal dosage (LD50) of the CFJY-623 isolate for crucian carp was determined as 1.31 × 107 CFU/mL. Artificial experimental infection showed that the CFJY-623 isolate caused considerable histological lesions in the fish, including tissue cell degeneration, necrosis, and inflammatory cell infiltrating. Drug sensitivity testing showed that the isolate was susceptible to aminoglycosides, carbapenemes, and nitrofurans. Exploring its growing features showed that this isolate exhibited a high level of environmental adaptability. These results provided a scientific basis for the identification of A. veronii and treatment for fish infected by this pathogen.

[The hemodynamic study of internal jugular vein in patients with pulsatile tinnitus by color doppler sonography]

Objective:To investigate the hemodynamic changes of internal jugular vein（IJV） in patients with pulsatile tinnitus（PT） detected by color doppler sonography（CDS）. To explore the correlation of PT with IJV drainage dominance and the value of CDS in the diagnosis of PT. Method:Two hundred and twenty-one patients with PT were examined with the CDS and IJV compression test. The hemodynamic data of the upper, middle and lower IJV were compared with both PT side and unaffected side. The correlation of the PT with the IJV drainage dominance was analyzed. Result:A total of 125 cases（56.6%） of 221 patients with PT underwent ultrasonic IJV compression test with positive results, 96 cases（43.3%） with negative results. In the positive compression test group, the tinnitus disappeared after IJV being completely compressed in 109 cases（87.2%）, and in 16 cases（12.8%） after IJV being partial closure. The extent of sectional area reduction was: upper jugular vein（75.41 ±9.39）%, middle jugular vein（80.25±13.16）%, lower jugular vein（86.58± 7.53）%. The blood flow volume on the tinnitus side was obviously higher than that on the unaffected side（P=0.001）. In the negative compression test group, there was no significant difference in blood flow volume between tinnitus side and unaffected side. In the IJV positive compression test group, 54 cases（43.2%） were IJV drainage dominance combined, and 71 cases（56.8%） were non-dominant combined. In the IJV negative compression test group, 24 cases（25%） were IJV drainage dominance combined, and 72 cases（75%） were non-dominant combined. Conclusion:The positive result of IJV compression test using CDS and the flow volume of IJV on the affected side significantly higher than that on the unaffected side contributed to the diagnosis of venous PT. In this study, the IJV non-dominant side was more common in the venous PT.

P4671A well-defined subgroup of chronic thromboembolic pulmonary hypertension patients are positive for antiphospholipid antibodies

Introduction

Recurrent thromboembolism is a major risk factor for chronic thromboembolic pulmonary hypertension (CTEPH). Antiphospholipid antibodies (aPL) are a recognized risk factor for recurrent thromboembolism, however, their contribution to the development of CTEPH is currently unknown.

Purpose

The aim of this study was to evaluate the prevalence of antiphospholipid autoantibodies in a large cohort of consecutive patients with CTEPH.

Methods

Starting May 2013 to December 2018, 297 CTEPHpatients were consecutively enrolled. Diagnosis was confirmed with standardized right heart catheterization, 2D or/and 3D pulmonary angiography in all patients.All patients were also screened for thrombophilia including lupus anticoagulant IgG/IgM anticardiolipin antibodies and IgG/IgM aβ2GPI antibodies. Clinical and demographic characteristics, laboratory profile and hemodynamic data were compared between patients with aPL positive and aPL negative laboratory profiles.

Results

Overall, 297 consecutive patients with CTEPH were assessed for aPLs. Of these, 23 patients (7.7%) resulted positive for laboratory tests exploring aPL. Among patients with positive aPL, profile 17 (74%) were positive for all three test exploring aPL (LA+, aCL+, aB2GPI+). When compared to CTEPH patients without aPL test positivity, those positive for aPL were significantly younger (30.0 vs 55.6 years, p<0.0001), had a positive history of pulmonary embolism (95.6% vs 65.7%, p=0.003), deep venous thrombosis (78.3% vs 41.9%, p=0.0008) and were more frequently affected by other autoimmune diseases (43.5% vs 2.9%, p<0.0001). Moreover, positive aPL patients showed better hemodynamics on right heart catheterization, had more proximal lesions, and had more frequently level I and II surgical classification (82.6% vs 40.5%, p=0.0002) on pulmonary angiography.

Conclusions

These findings suggest that young patients with pulmonary embolism should be assessed for aPLs to guide anticoagulation therapy and prevent recurrences. Additionally, younger age, more proximal lesions and less severe hemodynamic profiles make majority patients with APS good candidates for PEA surgery.

[Analysis of the effect and influencing factors of customized sound on tinnitus]

Objective:To explore the effect and influencing factors of customized sound on tinnitus. Method:303 patients with tinnitus who received customized sound therapy for 6 months were enrolled in this study. Tinnitus handicap inventory (THI) was used to evaluate the treatment effect before treatment, 1 month, 2 months, 3 months, 4 months, 5 months and 6 months after treatment, and the influencing factors of sound treatment effect were analyzed. Result:The THI score decreased at the 1, 2, 3, 4, 5 and 6 months after treatment (P<0.01), compared with that before treatment. Gender, tinnitus type and presence or absence of voice allergy had no effect on THI score before treatment and 6 months after treatment (P>0.05). Conclusion:Customized sound therapy can reduce the score of THI in tinnitus patients, which supports that sound therapy can reduce the negative impact and disturbances produced by tinnitus, and its curative effect is not affected by gender, tinnitus type and presence or absence of voice allergy..

Electrical stimulation shifts healing/scarring towards regeneration in a rat limb amputation model

Different species respond differently to severe injury, such as limb loss. In species that regenerate, limb loss is met with complete restoration of the limbs’ form and function, whereas in mammals the amputated limb’s stump heals and scars. In in vitro studies, electrical stimulation (EStim) has been shown to promote cell migration, and osteo- and chondrogenesis. In in vivo studies, after limb amputation, EStim causes significant new bone, cartilage and vessel growth. Here, in a rat model, the stumps of amputated rat limbs were exposed to EStim, and we measured extracellular matrix (ECM) deposition, macrophage distribution, cell proliferation and gene expression changes at early (3 and 7 days) and later stages (28 days). We found that EStim caused differences in ECM deposition, with less condensed collagen fibrils, and modified macrophage response by changing M1 to M2 macrophage ratio. The number of proliferating cells was increased in EStim treated stumps 7 days after amputation, and transcriptome data strongly supported our histological findings, with activated gene pathways known to play key roles in embryonic development and regeneration. In conclusion, our findings support the hypothesis that EStim shifts injury response from healing/scarring towards regeneration. A better understanding of if and how EStim controls these changes, could lead to strategies that replace scarring with regeneration.

Single-molecule characterization of extrinsic transcription termination by Sen1 helicase

Extrinsic transcription termination typically involves remodeling of RNA polymerase by an accessory helicase. In yeast this is accomplished by the Sen1 helicase homologous to human senataxin (SETX). To gain insight into these processes we develop a DNA scaffold construct compatible with magnetic-trapping assays and from which S. cerevisiae RNA polymerase II (Pol II), as well as E. coli RNA polymerase (ecRNAP), can efficiently initiate transcription without transcription factors, elongate, and undergo extrinsic termination. By stalling Pol II TECs on the construct we can monitor Sen1-induced termination in real-time, revealing the formation of an intermediate in which the Pol II transcription bubble appears half-rewound. This intermediate requires ~40 sec to form and lasts ~20 sec prior to final dissociation of the stalled Pol II. The experiments enabled by the scaffold construct permit detailed statistical and kinetic analysis of Pol II interactions with a range of cofactors in a multi-round, high-throughput fashion.

Yeast’s Sen1 helicase is involved in the suppression of antisense transcription from bidirectional eukaryotic promoters. Here authors develop and utilize a quantitative single-molecule assay reporting on the kinetics of extrinsic eukaryotic transcription termination by the Sen1 helicase and a reaction intermediate in which the Pol II transcription bubble appears half-rewound.

Key factors determining variations in RNA interference efficacy mediated by different double-stranded RNA lengths in Tribolium castaneum

Double-stranded RNA (dsRNA) length may affect RNA interference (RNAi) efficacy. Herein, variation in RNAi efficacy associated with dsRNA molecular length was confirmed via comparison of knockdown results following dsRNA injection into Tribolium castaneum. Through in vitro experiments with T. castaneum midgut, dsRNA accumulation in the midgut, degradation by midgut homogenates and persistence in haemolymph after injection were tested to determine the causes of RNAi efficacy variation. The comparative efficacies of dsRNAs were 480 bp ≈ 240 bp > 120 bp > 60 bp >> 21 bp. The combined midgut dsRNA accumulation and midgut homogenate-induced degradation analyses suggested cellular uptake to be the key barrier for 21 bp dsRNA functioning, but was likely not the main determinant of the variation in longer dsRNAs' (≥60 bp) bioactivity. In vitro RNAi experiment with T. castaneum midgut showed that long dsRNAs all significantly depleted the expression of corresponding genes, suggesting little variation in intracellular RNAi machinery's affinity for different dsRNA lengths. In vivo haemolymph content dynamics of different dsRNAs following injection indicated higher persistence of longer dsRNAs. In addition, comparison of the in vivo and in vitro RNAi efficacy also indicated the importance of haemolymph degradation. Thus, the varied efficacy of long dsRNAs resulted from their degradation by nucleases, which varied with dsRNA length.