Sequence Variation and Expression Analysis of Seed Dormancy- and Germination-Associated ABA- and GA-Related Genes in Rice Cultivars

Abscisic acid (ABA) and Gibberellic acid (GA) play key roles in regulating seed dormancy and germination. First, when examining germination of different rice cultivars, we found that their germination timing and dormancy status are rather distinct, coupled with different GA/ABA ratio. Second, we studied genomic sequences of ABA and GA dormancy- and germination-associated genes in rice and discovered single nucleotide polymorphisms and insertions/deletions (Indels) in both coding and regulatory sequences. We aligned all these variations to the genome assemblies of 9311 and PA64s and demonstrated their relevance to seed dormancy both quantitatively and qualitatively based on gene expression data. Third, we surveyed and compared differentially expressed genes in dry seeds between 9311 and PA64s to show that these differentially expressed genes may play roles in seed dormancy and germination

Intrinsic plasmids influence MicF-mediated translational repression of ompF in Yersinia pestis

Yersinia pestis, which is the causative agent of plague, has acquired exceptional pathogenicity potential during its evolution from Y. pseudotuberculosis. Two laterally acquired plasmids, namely, pMT1 and pPCP1, are specific to Y. pestis and are critical for pathogenesis and flea transmission. Small regulatory RNAs (sRNAs) commonly function as regulators of gene expression in bacteria. MicF, is a paradigmatic sRNA that acts as a post-transcriptional repressor through imperfect base pairing with the 5’-UTR of its target mRNA, ompF, in Escherichia coli. The high sequence conservation and minor variation in the RNA duplex of MicF-ompF has been reported in Yersinia. In this study, we utilized super-folder GFP reporter gene fusion to validate the post-transcriptional MicF-mediated regulation of target mRNA ompF in Y. pestis. Unexpectedly, upon MicF overexpression, the slightly upregulated expression of OmpF were found in the wild-type strain, which contradicted the previously established model. Interestingly, the translational repression of ompF target fusions was restored in the intrinsic plasmids-cured Y. pestis strain, suggesting intrinsic plasmids influence the MicF-mediated translational repression of ompF in Y. pestis. Further examination showed that plasmid pPCP1 is likely the main contributor to the reversal of MicF-mediated translational repression of ompF. It represents that the possible roles o

Quantitative testing of the methodology for genome size estimation in plants using flow cytometry: a case study of the Primulina genus

Flow cytometry (FCM) is a commonly used method for estimating genome size in many organisms. The use of flow cytometry in plants is influenced by endogenous fluorescence inhibitors and may cause an inaccurate estimation of genome size; thus, falsifying the relationship between genome size and phenotypic traits/ecological performance. Quantitative optimization of FCM methodology minimizes such errors, yet there are few studies detailing this methodology. We selected the genus Primulina, one of the most representative and diverse genera of the Old World Gesneriaceae, to evaluate the methodology effect on determining genome size. Our results showed that buffer choice significantly affected genome size estimation in six out of the eight species examined and altered the 2C-value (DNA content) by as much as 21.4%. The staining duration and propidium iodide (PI) concentration slightly affected the 2C-value. Our experiments showed better histogram quality when the samples were stained for 40 minutes at a PI concentration of 100 µg ml-1. The quality of the estimates was not improved by one-day incubation in the dark at 4 °C or by centrifugation. Thus, our study determined an optimum protocol for genome size measurement in Primulina: LB01 buffer supplemented with 100 µg ml-1 PI and stained for 40 minutes. This protocol also demonstrated a high universality in other Gesneriaceae genera. We report the genome size of nine Gesneriaceae species for the first time. The results showed substantial genome size variation both within and among the species, with the 2C-value ranging between 1.62 and 2.71 pg. Our study highlights the necessity of optimizing the FCM methodology prior to obtaining reliable genome size estimates in a given taxon

Nitrogen stimulates the growth of subsurface basalt-associated microorganisms at the western flank of the Mid-Atlantic Ridge

Oceanic crust constitutes the largest aquifer system on Earth, and microbial activity in this environment has been inferred from various geochemical analyses. However, empirical documentation of microbial activity from subsurface basalts is still lacking, particularly in the cool (<25 °C) regions of the crust, where are assumed to harbor active iron-oxidizing microbial communities. To test this hypothesis, we report the enrichment and isolation of crust-associated microorganisms from North Pond, a site of relatively young and cold basaltic basement on the western flank of the Mid-Atlantic Ridge that was sampled during Expedition 336 of the Integrated Ocean Drilling Program. Enrichment experiments with different carbon (bicarbonate, acetate, methane) and nitrogen (nitrate and ammonium) sources revealed significant cell growth (one magnitude higher cell abundance), higher intracellular DNA content, and increased Fe3+/ΣFe ratios only when nitrogen substrates were added. Furthermore, a Marinobacter strain with neutrophilic iron-oxidizing capabilities was isolated from the basalt. This work reveals that basalt-associated microorganisms at North Pond had the potential for activity and that microbial growth could be stimulated by in vitro nitrogen addition. Furthermore, iron oxidation is supported as an important process for microbial communities in subsurface basalts from young and cool ridge flank basement

Reconstruction and in silico analysis of an Actinoplanes sp. SE50/110 genome-scale metabolic model for acarbose production

Actinoplanes sp. SE50/110 produces the -glucosidase inhibitor acarbose, which is used to treat type 2 diabetes mellitus. To obtain a comprehensive understanding of its cellular metabolism, a genome-scale metabolic model of strain SE50/110, iYLW1028, was reconstructed on the bases of the genome annotation, biochemical databases, and extensive literature mining. Model iYLW1028 comprises 1028 genes, 1128 metabolites and 1219 reactions. 122 and 81 genes were essential for cell growth on acarbose synthesis and sucrose media, respectively, and the acarbose biosynthetic pathway in SE50/110 was expounded completely. Based on model predictions, the addition of arginine and histidine to the media increased acarbose production by 78% and 59%, respectively. Additionally, dissolved oxygen has a great effect on acarbose production based on model predictions. Furthermore, genes to be overexpressed for the overproduction of acarbose were identified, and the deletion of treY eliminated the formation of by-product component C. Model iYLW1028 is a useful platform for optimizing and systems metabolic engineering for acarbose production in Actinoplanes sp. SE50/110

Acid-base transport in pancreas – new challenges

Along the gastrointestinal tract a number of epithelia contribute with acid or basic secretions in order to aid digestive processes. The stomach and pancreas are the most extreme examples of acid (H+) and base (HCO3-) transporters, respectively. Nevertheless, they share the same challenges of transporting acid and bases across epithelia and effectively regulating their intracellular pH. In this review, we will make use of comparative physiology to enlighten the cellular mechanisms of pancreatic HCO3- and fluid secretion, which is still challenging physiologists. Some of the novel transporters to consider in pancreas are the proton pumps (H+-K+-ATPases), as well as the calcium-activated K+ and Cl- channels, such as KCa3.1 and TMEM16A/ANO1. Local regulators, such as purinergic signalling, fine-tune and coordinate pancreatic secretion. Lastly, we speculate whether dys-regulation of acid-base transport contributes to pancreatic diseases including cystic fibrosis, pancreatitis and cancer

Classification of ADHD children through multimodal Magnetic Resonance Imaging

Attention deficit/hyperactivity disorder (ADHD) is one of the most common diseases in school-age children. To date, the diagnosis of ADHD is mainly subjective and studies of objective diagnostic method are of great importance. Although many efforts have been made recently to investigate the use of structural and functional brain images for the diagnosis purpose, few of them are related to ADHD. In this paper, we introduce an automatic classification framework based on brain imaging features of ADHD patients, and present in detail the feature extraction, feature selection and classifier training methods. The effects of using different features are compared against each other. In addition, we integrate multimodal image features using multi-kernel learning (MKL). The performance of our framework has been validated in the ADHD-200 Global Competition, which is a world-wide classification contest on the ADHD-200 datasets. In this competition, our classification framework using features of resting-state functional connectivity was ranked the 6th out of 21 participants under the competition scoring policy, and performed the best in terms of sensitivity and J-statistic

A fluoroquinolone resistance associated mutation in gyrA affects DNA supercoiling in Campylobacter jejuni

The prevalence of fluoroquinolone (FQ)-resistant Campylobacter has become a concern for public health. To facilitate the control of FQ-resistant Campylobacter, it is necessary to understand the impact of FQ resistance on the fitness of Campylobacter in its natural hosts as understanding fitness will help to determine and predict the persistence of FQ-resistant Campylobacter. Previously it was shown that acquisition of resistance to FQ antimicrobials enhanced the in vivo fitness of FQ-resistant Campylobacter. In this study, we confirmed the role of the Thr-86-Ile mutation in GyrA in modulating Campylobacter fitness by reverting the mutation to the wild-type allele, which resulted in the loss of the fitness advantage. Additionally, we determined if the resistance-conferring GyrA mutations alter the enzymatic function of the DNA gyrase. Recombinant wild-type gyrase and mutant gyrases with three different types of mutations (Thr-86-Ile, Thr-86-Lys, and Asp-90-Asn), which are associated with FQ resistance in Campylobacter, were generated in E. coli and compared for their supercoiling activities using an in vitro assay. The mutant gyrase with the Thr-86-Ile change showed a greatly reduced supercoiling activity compared with the wild-type gyrase, while other mutant gyrases did not show an altered supercoiling. Furthermore, we measured DNA supercoiling within Campylobacter cells using a reporter plasmid. Consistent with the results from the in vitro supercoiling assay, the FQ-resistant mutant carrying the Thr-86-Ile change in GyrA showed much less DNA supercoiling than the wild-type strain and the mutant strains carrying other mutations. Together, these results indicate that the Thr-86-Ile mutation, which is predominant in clinical FQ-resistant Campylobacter, modulates DNA supercoiling homeostasis in FQ-resistant Campylobacter

Dopaminergic neuronal differentiation from the forebrain-derived human neural stem cells induced in cultures by using a combination of BMP-7 and pramipexole with growth factors

Transplantation of dopaminergic (DA) neurons is considered to be the most promising therapeutic strategy for replacing degenerated dopamine cells in the midbrain of Parkinson’s disease (PD), thereby restoring normal neural circuit function and slow clinical progression of the disease. Human neural stem cells (hNSCs) derived from fetal forebrain are thought to be the important cell sources for producing DA neurons because of their multipotency for differentiation and long-term expansion property in cultures. However, low DA differentiation of the forebrain-derived hNSCs limited their therapeutic potential in PD. In the current study, we explored a combined application of Pramipexole (PRX), bone morphogenetic proteins 7 (BMP-7), and growth factors, including acidic fibroblast factor (aFGF), forskolin, and phorbol-12-myristae-13-acetate (TPA), to induce differentiation of forebrain-derived hNSCs towards DA neurons in cultures. We found that DA neuron-associated genes, including Nurr1, Neurogenin2 (Ngn2), and tyrosine hydroxylase (TH) were significantly increased after 24h of differentiation by RT-PCR analysis (p<0.01). Fluorescent examination showed that about 25% of cells became TH-positive neurons at 24h, about 5% of cells became VMAT2 (vascular monoamine transporter 2)-positive neurons, and less than 5% of cells became DAT (dopamine transporter)-positive neurons at 72h following differentiation in cultures. Importantly, these TH-， VMAT2- and DAT-expressing neurons were able to release dopamine into cultures under both of the basal and evoked conditions. Dopamine levels released by DA neurons produced using our protocol were significantly higher compared to the control groups (P<0.01), as examined by ELISA. Our results demonstrated that the combination of PRX, BMP-7, and growth factors was able to greatly promote differentiation of the forebrain-derived hNSCs into DA-releasing neurons

Birthdate study of GABAergic neurons in the lumbar spinal cord of the glutamic acid decarboxylase 67-green fluorescent protein knock-in mouse

Despite the abundance of studies on γ-aminobutyric acid (GABA) ergic neuron distribution in the mouse developing spinal cord, no investigation has been devoted so far to their birthdates. In order to determine the spinal neurogenesis of a specific phenotype, the GABAergic neurons in the spinal cord, we injected bromodeoxyuridine (BrdU) at different developmental stages of the glutamic acid decarboxylase (GAD)67-green fluorescent protein (GFP) knock-in mice. We thus used GFP to mark GABAergic neurons and labeled newly born cells with the S-phase marker BrdU at different embryonic stages. Distribution of GABAergic neurons labeled with BrdU was then studied in spinal cord sections of 60-day old mice. Our birthdating studies revealed that GABAergic neurogenesis was present at embryonic day 10.5 (E10.5). Since then, the generation of GABAergic neurons significantly increased, and reached a peak at E11.5. Two waves for the co-localization of GABA and BrdU in the spinal cord were seen at E11.5 and E13.5 in the present study. The vast majority of GABAergic neurons were generated before E14.5. Thereafter, GABA-positive neuron generation decreased drastically. The present results showed that the birthdates of GABAergic neurons in each lamina were different. The peaks of GABAergic neurogenesis in lamina Ⅱ were at E11.5 and E13.5, while in lamina I and III, they were at E13.5 and E12.5 respectively. The present results suggest that the birthdates of GABAergic neurons vary in different lamina and follow a specific temporal sequence. This will provide valuable information for future functional studies