Difference Analysis Based on 16S rRNA Sequencing of Different Soil Bacterial Communities

Abstract

Objective To study the structure and differences of bacterial communities in different soils, and to explore the effectiveness of 16S rRNA sequencing in identification of different soil. Methods Soil samples from 7 places in Shanghai were collected, then bacterial genomic DNA were extracted from them. The fragments of hypervariable region from 16S rRNA sequences were sequenced with high-throughput sequencing techniques. The results were quantified or visualized with bioinformatics software. The differences in diversity and abundance among the three kinds of bacterial communities in soil samples from grassland, forests and beaches were compared and analyzed. Results The statistical differences that existed among the alpha diversity indexes of bacterial communities in soil samples of grassland, forests and beaches had statistical significance. The relative abundance and diversity of bacterial communities in these three kinds of soil were significantly different. Grassland soil had higher Acidobacteria abundance, forest soil had higher Proteobacteria abundance, beach soil had higher Actinobacteria abundance. However, the differences in soil bacterial communities in artificial grasslands, natural grasslands and industrial district grasslands did not have statistical significance. Conclusion 16S rRNA sequencing can effectively distinguish different soils. This method may be able to provide clues for first crime scene inference in criminal cases.

Progress in the 16S rRNA Gene Sequencing in Forensic Science

Forensic microorganism is one of the hotspots of forensic science research. Due to its conservatism and specificity, the 16S rRNA gene is found to be an ideal marker for forensic identification. With the rapid development of high throughput sequencing technology, the research on microorganisms has been gradually applied to many fields such as environment and health care. In the field of forensic science, the results of forensic microbiology research, represented by 16S rRNA gene sequencing, are also gradually applied to forensic practice, such as biological samples identification, individual identification, postmortem interval estimation, and regional inference, which not only provide clues for the investigation of cases but also complement and assist traditional methods. This paper describes the research methods and related sequencing technologies of 16S rRNA gene sequencing, summarizes its research progress, and discusses the application value and potential of 16S rRNA in forensic science.

Determination of the potential of induced pluripotent stem cells to differentiate into mouse nucleus pulposus cells in vitro

We determined the potential for induced pluripotent stem (iPS) cells to differentiate into nucleus pulposus (NP)-like cells in mice. iPS cells were generated from tail-tip fibroblasts. We used a pellet culture model with the aim of determining the applicability of iPS cell-based therapy to intervertebral disc degeneration (IVD). The cell pellet was cultured in an NP cell basal medium comprising Dulbecco's modified Eagle's medium supplemented with transforming growth factor beta 1, dexamethasone, ascorbate-2-phosphate, and 1% ITS-Premix. The pellet was evaluated by quantitative reverse transcription polymerase chain reaction, immunohistochemical staining, and biochemical composition. The differentiation of iPS cells into NP cells was demonstrated by the protein and mRNA expression levels of proteoglycan, collagen II, aggrecan, and CD24. Furthermore, increased hydroxyproline content and dimethylmethylene blue staining demonstrated that the collagen II and glycosaminoglycan content in the NP cells increased with time. We have shown that cultured mouse iPS cells can be induced to differentiate into NP cells. Such proof-of-concept opens up the possibility of producing patient-specific NP cells in a relatively simple and straightforward manner with high efficiency. We are confident that such cells could be immediately useful for the study of IVD disease.

Therapeutic potential of spinal cord stimulation for gastrointestinal motility disorders: a preliminary rodent study

BACKGROUND

Spinal cord electrical stimulation (SCS) has been applied for the management of chronic pain. Most of studies have revealed a decrease in sympathetic activity with SCS. The aim of this study was to investigate the effects and mechanisms of SCS on gastrointestinal (GI) motility in healthy and diabetic rats.

METHODS

Male rats chronically implanted with a unipolar electrode at T9/T10 were studied. The study included four experiments to assess the effects of SCS on (1) gastric tone; (2) gastric emptying of liquids and intestinal transit; (3) gastric emptying of solids; and (4) sympathovagal balance in healthy rats and/or in Streptozotocin (STZ)-induced diabetic rat.

KEY RESULTS

(1) Spinal cord stimulation intensity dependently increased gastric tone in healthy rats. The gastric volume was 0.97 ± 0.15 mL at baseline, and decreased to 0.92 ± 0.16 mL with SCS of the 30% motor threshold (MT; p = 0.13 vs baseline), 0.86 ± 0.14 mL with 60% MT (p = 0.045 vs baseline), and 0.46 ± 0.19 mL with 90% MT (p = 0.0050 vs baseline). (2) Spinal cord stimulation increased gastric emptying of liquids by about 17% and accelerated small intestinal transit by about 20% in healthy rats (p < 0.001). (3) Spinal cord stimulation accelerated gastric emptying of solids by about 24% in healthy rats and by about 78% in diabetic rats. (4) Spinal cord stimulation decreased sympathetic activity (1.13 ± 0.18 vs 0.68 ± 0.09, p < 0.04) and sympathovagal balance (0.51 ± 0.036 vs 0.40 ± 0.029, p = 0.028).

CONCLUSIONS & INFERENCES

Spinal cord stimulation accelerates gastric emptying of liquids and solids, and intestinal transit, probably by inhibiting the sympathetic activity. Spinal cord stimulation may have a therapeutic potential for treating GI motility disorders.

Effects and mechanisms of vaginal electrical stimulation on gastric tone in dogs

Electrical stimulation of one part of the gut may have beneficial or adverse effects on another region. We hypothesized that electrical stimulation of a visceral organ in one system might have an effect on another visceral organ system. That is, disorders of one system may be treated by interventions of another system and this may lead to a more convenient or less invasive therapies in some cases. The aim of this study was to evaluate the effects and mechanisms of vaginal electrical stimulation (VES) with different parameters on gastric tone and gastric slow waves in conscious dogs. Seven dogs were studied in two experiments. Experiment 1 was to study effects of VES on gastric tone and slow waves. Experiment 2 was performed in two sessions (long pulse VES plus guanethidine and VES with trains of long pulse plus guanethidine) to study involvements of possible sympathetic mechanisms. The results of our experiments were: (i) VES increased the gastric volume in a dose-dependent manner with the increase of stimulation frequency, amplitude or pulse width; (ii) VES had no effects on gastric slow waves; (iii) the inhibitory effect of VES with long pulses or trains of long pulses on gastric tone was abolished by guanethidine; and (iv) few or mild symptoms were noted with stimulation. VES decreases proximal gastric tone in an energy-dependent manner without affecting gastric slow waves. The inhibitory effect of VES is mediated by a sympathetic pathway. Hypertensive gastric tone might be treated using electrical stimulation of the vagina which is minimally invasive.

Healing of severe reflux esophagitis with PPI does not improve esophageal dysmotility

Esophageal dysmotility is frequently associated with gastroesophageal reflux disease (GERD). The aim of this study was to investigate the relationship between the severity of reflux esophagitis and esophageal dysmotility and evaluate the effect of prolonged treatment with proton pump inhibitor (lansoprazole 30 mg/day) on esophageal motility in patients with severe reflux esophagitis associated with esophageal motility disorder. Twelve healthy subjects (HS) and 100 patients with reflux disease were involved in the study consisting of two parts: (i) comparison of esophageal motility in HS and patients with non-eroseive reflux disease (NERD), mild esophagitis and severe esophagitis; (ii) effect of 3-6 months lansoprazole therapy on esophageal motility in 23 patients with severe esophagitis, pathologic acid reflux and esophageal peristaltic dysfunction. Results included the following. (i) Esophageal dysmotility was noted in both patients with NERD and erosive GERD. (ii) Severe esophagitis was associated with severe esophageal dysmotility. (iii) Healing of severe esophagitis did not improve esophageal dysmotility. The resting lower esophageal sphincter pressure was 3.9 mmHg (range 1.7-20) before treatment and 4.8 mmHg (range 1.2-18.3) after esophagitis healing (P = 0.23, vs. before treatment), the amplitude of distal esophageal contraction was 28.8 mmHg (range 10.9-80.6) before treatment and 33.3 mmHg (range 10.0-72.5) after esophagitis healing (P = 0.59, vs. before treatment) and the frequency of failed peristalsis was 70% (range 0-100%) before treatment and 70% (range 0-100%) after esophagitis healing (P = 0.78, vs. before treatment). Both esophageal motility disorders and acid reflux play important roles in the mechanism of GERD, especially in severe esophagitis. Esophageal dysmotility is not secondary to acid reflux and esophagitis; it should be a primary motility disorder.

Fortisterol, a novel steroid with an unusual seven-membered lactone ring B from the Chinese marine sponge Biemna fortis Topsent

Fortisterol (1), a novel steroid with a rare seven-membered lactone ring B, has been isolated from the marine sponge Biemna fortis and its structure gas been elucidated on the basis of spectroscopic data.

[Treatment of femoral neck fractures in the elderly patients with the compression screw]

The treatment of 50 patients above 70 years with femoral neck fractures were reviewed. All the patients were treated by internal fixation with the compression screw. Followed-up 1-5 years reviews showed that the rate of fracture union was 83%, the satisfactory rate of the function was 96%, no death was found. It is suggested that internal fixation with compression screw may be a good treatment in the elderly patients with femoral neck fractures.

Routine cryopreservation of kiwifruit (Actinidia spp) germplasm by encapsulation-dehydration: importance of plant growth regulators

The encapsulation-dehydration protocol was optimized for an in vitro cultured hybrid Actinidia arguta x A. deliciosa. Shoot tips from 14-d reactivated mononodal microcuttings were embedded, transferred to liquid culture medium whose sucrose concentration was daily increased (0.3, 0.5, 0.75 M) and then kept at 0.75 M for 2 or 4 d. Dehydration on silica gel was monitored to 20+/-1.5% residual water content (dry weight basis), allowing direct quenching in liquid nitrogen and rewarming at room temperature. Differential scanning calorimetry analysis underlined the importance of reversible glass transition in shoots for survival. Regrowth ranged from 85% to 95%. Growing shoot tips showed no phenotypic abnormalities. Rooting was also achieved. This method was routinely applied to diploid A. chinensis and A. eriantha, and to several diploid hybrids, yielding over 70% regrowth. A slight decrease in sucrose molarity (0.65 M) allowed tetraploid A. chinensis and A. chrysantha x A. arguta to survive dehydration, but not quenching in LN. For A. deliciosa cv Hayward and cv Tomuri, normal regrowth after cryopreservation was achieved only after modification of the pre- and post-culture media, highlighting the importance of monitoring plant growth regulator balance, principally at the post-thaw recovery step.

A binding site peptide fragment of the nicotinic acetylcholine receptor. Sequence-specific assignment of 1H-NMR resonances in the dodecamer alpha 185-196

The total sequence-specific 1H assignment for the alpha 185-peptide was accomplished by analysis of COSY spectra along with spin-decoupling and confirmatory NOE difference experiments. Some ambiguities in the assignments were successfully addressed utilizing additional peptides with selective amino acid substitutions. The chemical shifts of several of the C alpha H resonances, along with evidence for a slowly exchanging amide at Thr-191 suggest that the alpha 185-peptide may contain a certain amount of non-random coil structure. The role of any such ordered structure in the mechanism of binding to alpha-bungarotoxin remains to be determined. The assignment of the peptide 1H resonances will facilitate the analysis and identification of chemical shift perturbations observed upon formation of the complex between alpha-bungarotoxin and the alpha 185-peptide [7].

Pseudolaric acids from Pseudolarix kaempferi

Three novel diterpenoids, pseudolaric acids A, B and C, were isolated from the root bark of Pseudolarix kaempferi Gorden used as an antifungal agent in folk medicine in China. The structures of pseudolaric acids B and C were assigned as 1 and 6 by spectral and chemical evidence. Pseudolaric acids A, B and C possess antifungal activity and pseudolaric acid B possesses an antifertility effect.