Identification of extracellular miRNA in human cerebrospinal fluid by next-generation sequencing

There has been a growing interest in using next-generation sequencing (NGS) to profile extracellular small RNAs from the blood and cerebrospinal fluid (CSF) of patients with neurological diseases, CNS tumors, or traumatic brain injury for biomarker discovery. Small sample volumes and samples with low RNA abundance create challenges for downstream small RNA sequencing assays. Plasma, serum, and CSF contain low amounts of total RNA, of which small RNAs make up a fraction. The purpose of this study was to maximize RNA isolation from RNA-limited samples and apply these methods to profile the miRNA in human CSF by small RNA deep sequencing. We systematically tested RNA isolation efficiency using ten commercially available kits and compared their performance on human plasma samples. We used RiboGreen to quantify total RNA yield and custom TaqMan assays to determine the efficiency of small RNA isolation for each of the kits. We significantly increased the recovery of small RNA by repeating the aqueous extraction during the phenol-chloroform purification in the top performing kits. We subsequently used the methods with the highest small RNA yield to purify RNA from CSF and serum samples from the same individual. We then prepared small RNA sequencing libraries using Illumina’s TruSeq sample preparation kit and sequenced the samples on the HiSeq 2000. Not surprisingly, we found that the miRNA expression profile of CSF is substantially different from that of serum. To our knowledge, this is the first time that the small RNA fraction from CSF has been profiled using next-generation sequencing.     

The spatiotemporal dynamics of Tribolium castaneum (Herbst): adult flight and gene flow

Tribolium castaneum (Herbst) has been used as a model organism to develop and test important ecological and evolutionary concepts and is also a major pest of grain and grain products globally. This beetle species is assumed to be a good colonizer of grain storages through anthropogenic movement of grain, and active dispersal by flight is considered unlikely. Studies using T. castaneum have therefore used confined or walking insects. We combine an ecological study of dispersal with an analysis of gene flow using microsatellites to investigate the spatiotemporal dynamics and adult flight of T. castaneum in an ecological landscape in eastern Australia. Flying beetles were caught in traps at grain storages and in fields at least 1 km from the nearest stored grain at regular intervals for an entire year. Significantly more beetles were trapped at storages than in fields, and almost no beetles were caught in native vegetation reserves many kilometres from the nearest stored grain. Genetic differentiation between beetles caught at storages and in fields was low, indicating that although T. castaneum is predominantly aggregated around grain storages, active dispersal takes place to the extent that significant gene flow occurs between them, mitigating founder effects and genetic drift. By combining ecological and molecular techniques, we reveal much higher levels of active dispersal through adult flight in T. castaneum than previously thought. We conclude that the implications of adult flight to previous and future studies on this model organism warrant consideration.     

Ellagic acid inhibits PDGF-BB-induced vascular smooth muscle cell proliferation and prevents atheroma formation in streptozotocin-induced diabetic rats

Plant-derived polyphenolic compounds have beneficial health effects. In the present study, we determined the ability of ellagic acid (EA) to prevent platelet-derived growth factor-BB (PDGF-BB)-induced proliferation of primary cultures of rat aortic smooth muscle cells (RASMCs). We also determined the ability of EA to prevent atherosclerosis in streptozotocin-induced diabetic rats. Proliferation of cells was measured via Alamar Blue assay and through propidium iodide-based cell cycle analysis in flow cytometer. Reactive oxygen species (ROS) were measured via 2′,7′-dichlorofluorescin diacetate and Amplex red methods. Expression of proliferation markers and activation of kinases were assessed by immunoblot analysis. Cotreatment of primary cultures of RASMCs with 25 μmol/L of EA significantly reduced PDGF-BB (20 ng/ml)-induced proliferation by blocking S-phase entry. EA effectively blocked PDGF receptor-β (PDGFR-β) tyrosine phosphorylation, generation of intracellular ROS and downstream activation of extracellular signal-regulated kinase 1/2. It also blocked PDGF-BB-induced expression of cyclin D1. Computational molecular docking of EA with the PDGFR-β–PDGF-BB complex revealed two putative inhibitor binding sites which showed similar binding energies with the known PDGFR-β inhibitor AG1295. In diabetic rats, supplementation of diet with 2% EA significantly blocked diabetes-induced medial thickness, and lipid and collagen deposition in the arch of aorta. These were assessed through haematoxylin and eosin, Oil Red O and Masson’s trichome staining, respectively. EA treatment also blocked cyclin D1 expression in medial smooth muscle cells in experimental animals. Thus, EA is effective in reducing atherosclerotic process by blocking proliferation of vascular smooth muscle cells.     

Effect of temperature on the survival of Aconophora compressa Walker (Hemiptera: Membracidae): implications for weed biocontrol

Abstract  In weed biocontrol, similarity of abiotic factors between the native and introduced range of a biocontrol agent is critical to its establishment and effectiveness. This is particularly the case for weeds that have a wide geographical distribution in the native range. For such weeds, the choice of a specialist insect that has narrow tolerance limits to important abiotic factors can diminish its ability to be an effective biocontrol agent. The membracid Aconophora compressa was introduced in Australia from Mexico for biocontrol of Lantana camara , a plant with a wide climatic tolerance. In this study we investigated the effect of constant and alternating temperatures on A. compressa survival. Longevity of adults and nymphs declined with increasing temperatures, and at 39°C individuals survived for less than a day. At lower temperatures, nymphs survived longer than adults. Survival at alternating temperatures was longer than at constant temperatures, but the general trend of lower survival at higher temperatures remained. Spatially and temporally, the climatic tolerance of A. compressa appears to be a subset of that of lantana, thereby limiting its potential impact.     

Stakeholder survey reveals priorities for African boxthorn biocontrol research in Australia

ABSTRACT

Insufficient engagement with stakeholders and regulators has been identified as a limiting factor for effective adoption of biocontrol globally. A survey was conducted to engage stakeholders affected by African boxthorn, to ask them about their perceived impacts of the weed and management expectations from biocontrol. Management objectives gleaned from the survey now guide selection and evaluation of candidate biocontrol agents for African boxthorn in Australia. Surveys such as this are an inexpensive way to understand how biocontrol can most effectively intersect with stakeholder perceptions and management priorities, and are likely to facilitate the acceptance and adoption of biocontrol.     

Deep learning-based image processing in optical microscopy

Optical microscopy has emerged as a key driver of fundamental research since it provides the ability to probe into imperceptible structures in the biomedical world. For the detailed investigation of samples, a high-resolution image with enhanced contrast and minimal damage is preferred. To achieve this, an automated image analysis method is preferable over manual analysis in terms of both speed of acquisition and reduced error accumulation. In this regard, deep learning (DL)-based image processing can be highly beneficial. The review summarises and critiques the use of DL in image processing for the data collected using various optical microscopic techniques. In tandem with optical microscopy, DL has already found applications in various problems related to image classification and segmentation. It has also performed well in enhancing image resolution in smartphone-based microscopy, which in turn enablse crucial medical assistance in remote places.Graphical abstract     

Vasoactive Intestinal Polypeptide-Related Peptides Modulate Tyrosine Hydroxylase Gene Expression in PC12 Cells Through Multiple Adenylate Cyclase-Coupled Receptors

Abstract: We investigated the receptor mechanisms by which vasoactive intestinal polypeptide (VIP) and related peptides exert their effects on tyrosine hydroxylase (TH) gene expression. VIP, secretin, and peptide histidine isoleucine (PHI) each produced increases in TH gene expression, as measured by increases in TH mRNA levels and TH activity. The concentrations at which the effects of these peptides were maximal differed for TH activity and TH mRNA. Moreover, maximal increases in TH activity were 130-140% of control, whereas maximal increases in TH mRNA were 250% of control. The concentration dependence of the increases in TH mRNA in response to the three peptides was analyzed by fitting the data to nonlinear regression models that assume either one or two components to the response. The data for secretin fit best to a model that assumes a single component to the increase in TH mRNA levels. The data derived for PHI and VIP fit best to models that assumed two components to the TH mRNA response. These data suggested that there may be more than one receptor or signal transduction mechanism involved in the response to the various peptides. We examined whether the peptides exerted their effects through common or multiple second messenger systems. The ability of maximally active concentrations of these peptides to stimulate increases in TH mRNA was not additive, indicating that the peptides work through a common receptor or signal transduction pathway. Each peptide stimulated increases in protein kinase A (PKA) activity. Secretin and VIP were ineffective in increasing TH mRNA levels in a PKA-deficient mutant PC12 cell line (A 126-1B2). Moreover, the adenylate cyclase antagonist 2′,5′-dideoxyadenosine prevented the increase in TH mRNA produced by each peptide. Thus, each peptide requires an intact cyclic AMP second messenger pathway to produce changes in TH gene expression, suggesting that the complex pattern of response to VIP and PHI revealed by concentration-response analysis was due to the actions of these peptides at multiple receptors. To evaluate this possibility, we examined the effect of several peptide receptor antagonists on the increase in TH gene expression elicited by VIP, PHI, and secretin. The secretin antagonist secretin (5–27) (20 μM) had no significant effect on VIP or PHI stimulation of TH gene expression, but reduced the effect of secretin. The VIP antagonist VIP (10–28) (20 μM) reduced the effect of VIP on increasing TH mRNA, but had no significant effect on the response of TH mRNA to secretin or PHI. Interestingly, the VIP antagonist [Ac-Tyr¹,D-Phe²]-growth hormone releasing factor [GRF(1–29)] amide (20 μM) potentiated the effect of VIP on elevating TH mRNA levels, but had no effect on secretin-stimulated TH mRNA induction. To determine whether this response was mediated through the cyclic AMP pathway, we examined the effects of the VIP antagonist [Ac-Tyr¹,D-Phe²]-GRF(1–29) amide on VIP stimulation of PKA activity. Although the antagonist had no effect alone, it enhanced stimulation of PKA activity by VIP. Taken together, these findings indicate that VIP and secretin stimulate TH mRNA through different adenylate cyclase-linked receptors and that a second VIP receptor may modulate TH induction by inhibiting VIP stimulation of PKA.     

Three new small nucleolar RNAs that are psoralen cross-linked in vivo to unique regions of pre-rRNA.

We have recently described three novel human small nucleolar RNA species with unique nucleotide sequences, which were named E1, E2, and E3. The present article describes specific psoralen photocross-linking in whole HeLa cells of E1, E2, and E3 RNAs to nucleolar pre-rRNA. These small RNAs were cross-linked to different sections of pre-rRNA. E1 RNA was cross-linked to two segments of nucleolar pre-rRNA; one was within residues 697 to 1163 of the 5' external transcribed spacer, and the other one was between nucleotides 664 and 1021 of the 18S rRNA sequence. E2 RNA was cross-linked to a region within residues 3282 to 3667 of the 28S rRNA sequence. E3 RNA was cross-linked to a sequence between positions 1021 and 1639 of the 18S rRNA sequence. Primer extension analysis located psoralen adducts in E1, E2, and E3 RNAs that were enriched in high-molecular-weight fractions of nucleolar RNA. Some of these psoralen adducts might be cross-links of E1, E2, and E3 RNAs to large nucleolar RNA. Antisense oligodeoxynucleotide-targeted RNase H digestion of nucleolar extracts revealed accessible segments in these three small RNAs. The accessible regions were within nucleotide positions 106 to 130 of E1 RNA, positions 24 to 48 and 42 to 66 of E2 RNA, and positions 7 to 16 and about 116 to 122 of E3 RNA. Some of the molecules of these small nucleolar RNAs sedimented as if associated with larger structures when both nondenatured RNA and a nucleolar extract were analyzed.     

Impact of floral herbivory by <Emphasis Type="Italic">Coleotechnites eryngiella</Emphasis> Bottimer (Lepidoptera: Gelechiidae) on the reproductive output of <Emphasis Type="Italic">Eryngium yuccifolium</Emphasis> Michaux (Apiaceae): a test of the reserve ovary model

The reserve ovary model is a key hypothesis proposed to explain why plants produce surplus flowers and posits that plants may utilize surplus flowers to compensate for losses from floral herbivory. We tested this hypothesis in the prairie plant Eryngium yuccifolium and its floral herbivore Coleotechnites eryngiella. At five Illinois tallgrass prairie sites, we collected central, primary lateral, and secondary lateral inflorescences from E. yuccifolium to determine whether damage by the larvae of C. eryngiella to the flowers in earlier developing inflorescences would be compensated for in later developing inflorescences. Coleotechnites eryngiella does extensive damage to the central and primary inflorescences and little damage to the secondary inflorescences. Later maturing inflorescences did not compensate for early damage by increasing seed production in later inflorescences. The secondary inflorescences of E. yuccifolium may only compensate for catastrophic damage done to the central and primary inflorescences early on in development, serve as additional advertisements for pollinators, act as pollen donors, or allow the plant to take advantage of “ecological windows” of high pollinator and low herbivore abundance. Our findings were spatially and temporally consistent and did not support the predictions of the reserve ovary model in the E. yuccifolium–C. eryngiella system suggesting that in this system, alternate, proximate, and ultimate causes need to be explored for the production of surplus flowers.