Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing

Biological monitoring has failed to develop from simple binary assessment outcomes of the impacted/unimpacted type, towards more diagnostic frameworks, despite significant scientific effort over the past fifty years. It is our assertion that this is largely because of the limited information content of biological samples processed by traditional morphology-based taxonomy, which is a slow, imprecise process, focused on restricted groups of organisms. We envision a new paradigm in ecosystem assessment, which we refer to as ‘Biomonitoring 2.0’. This new schema employs DNA-based identification of taxa, coupled with high-throughput DNA sequencing on next-generation sequencing platforms. We discuss the transformational nature of DNA-based approaches in biodiversity discovery and ecosystem assessment and outline a path forward for their future widespread application.     

Comparative modeling of CCRL1, a key protein in masked immune diseases and virtual screening for finding inhibitor of this protein

Human CCRL1 belongs to the family of silent chemokine receptors. This transmembrane protein plays a role in blunting function of chemokines through binding to them. This will attenuate immune responses. Interaction between CCRL1 and CCL21 determines this immune extinction. Thus inhibiting the action of this atypical chemokine seems to stimulate immune responses especially in the case of suppressed and immune deficient conditions. In this study we predicted 3D structure of CCRL1 using comparative modeling and Hiddebn Markov Model algorithm. Final predicted model optimized by Modeller v9.8 and minimized regarding energy level using UCSF chimera candidate version1.5.3. ClasPro webserver was used to find interacting residues between CCRL1 and CCL21. Interacting residues were used as target for chemical inhibitors by simulated docking study. For finding potential inhibitors, library of KEGG compounds screened and 97 obtained chemicals docked against interacting residues between CCRL1- CCL21 and MolDock was used as docking scoring function. Results indicated that Hexadecanal is a potential inhibitor of CCRL1- CCL21 interaction. Inhibition of this interaction will increase intercellular level of CCl21 and interaction between CCL21 and CCR7 causes immune potentiaiton.     

Scaling up: A guide to high‐throughput genomic approaches for biodiversity analysis

The purpose of this review is to present the most common and emerging DNA‐based methods used to generate data for biodiversity and biomonitoring studies. As environmental assessment and monitoring programmes may require biodiversity information at multiple levels, we pay particular attention to the DNA metabarcoding method and discuss a number of bioinformatic tools and considerations for producing DNA‐based indicators using operational taxonomic units (OTUs), taxa at a variety of ranks and community composition. By developing the capacity to harness the advantages provided by the newest technologies, investigators can “scale up” by increasing the number of samples and replicates processed, the frequency of sampling over time and space, and even the depth of sampling such as by sequencing more reads per sample or more markers per sample. The ability to scale up is made possible by the reduced hands‐on time and cost per sample provided by the newest kits, platforms and software tools. Results gleaned from broad‐scale monitoring will provide opportunities to address key scientific questions linked to biodiversity and its dynamics across time and space as well as being more relevant for policymakers, enabling science‐based decision‐making, and provide a greater socio‐economic impact. As genomic approaches are continually evolving, we provide this guide to methods used in biodiversity genomics.     

Clinical response to chemotherapy in locally advanced breast cancer was not associated with several polymorphisms in detoxification enzymes and DNA repair genes

The main aim of the present study was to investigate the association between several genetic polymorphisms (in glutathione S-transferase members and DNA repair genes) and clinical response to chemotherapy in locally advanced breast cancer. A sequential series of 101 patients were prospectively included in this study. Clinical assessment of treatment was accomplished by comparing initial tumor size with preoperative tumor size using revised RECIST guideline (version 1.1). Clinical response was regarded as a response or no response. There was no difference between non-responders and responders for the prevalence of genotypes of the study polymorphisms.     

Some physiological and morphological responses of Pyrus boissieriana to flooding

European pear is a flooding-sensitive species, and for its cultivation in lowland areas, it is necessary to carry out the grafting of scions of commercial pear varieties into rootstocks belonging to flooding-tolerant wild pear species. Flooding tolerance of Pyrus boissieriana—a type of wild pear—was studied as a promissory rootstock for commercial pear. For this purpose, 3-month-old plants of P. boissieriana were subjected for 30 days to control (C), well-irrigated treatment, short-term (15 days) flooding plus 15 days recovery (F + R) and long-term (30 days) continuous flooding (F). Physiological performance, plant morphological changes and biomass accumulation were assessed. Results showed that, although stomatal conductance, transpiration and photosynthesis were progressively decreased by flooding, when flooding was short term (i.e., 2 weeks, F + R treatment) plants were able to adequately recover their physiological activity (50–74 % with respect to controls). In contrast, when plants continued to be flooded (F treatment), the physiological activity became null and the plants died quickly after the water subsided. Adventitious rooting was the most conspicuous registered morphological response to flooding, despite that flooded plants had shorter shoots and roots than control plants. Leaf and root biomass were 63 and 89 % higher under short-term flooding (F + R) than under continuous flooding (F), condition in which plants did not survive. In conclusion, P. boissieriana appears to be a promising species for its use as rootstock of commercial pear in lowland areas prone to flooding of up to 2 weeks. However, if the flooding period is extended, plants of this species are at risk of perishing.     

Microencapsulation by Spray Coagulation of Diltiazem HCl in Calcium Alginate-Coated Chitosan

The aim of this work was to develop a procedure for encapsulation of diltiazem HCl by spray coagulation. Factors affecting the formulations such as the effect of NaCl on the solubility of diltiazem in alginate solution, surface tension, pH, viscosity of the coagulation medium, and the effect of drug load on drug release were studied. The drug load was increased substantially from 10 up to 320 mg/mL by adding 1.2% w/v NaCl in 1% w/v alginate solution. More stable microcapsules were obtained at pH 4.6 (acetate buffer) than at a pH 2.8 (lactic acid), and the microencapsulation process was favored by the type of chitosan that produced low turbidity and viscosity in the coagulation medium. A dose of 50 mg/mL of diltiazem HCl, 1.2% w/v NaCl, and chitosan CS allowed higher amount of drug to be encapsulated. The high water solubility of diltiazem HCl leads to fast release from the microcapsules.     

Investigating the Effect of Heavy Metals on Developmental Stages of Anther and Pollen in <Emphasis Type="Italic">Chenopodium botrys</Emphasis> L. (Chenopodiaceae)

Excessive amounts of heavy metals adversely affect plant growth and development. Whereas some regions naturally contain high levels of heavy metals, anthropogenic release of heavy metals into the environment continuously increases soil contamination. Preliminary studies have shown that Chenopodium botrys can grow in some heavy metal contaminated soils and is a high accumulator plant species for Cu and moderately accumulator plant species for Fe, Mn, and Zn, thus, was considered as an important species in this study. Based on that, in this species, we studied the individual effects of heavy metals on the formation, development, and structure of anther and pollen. To achieve this purpose, surrounding area of Hame-Kasi iron and copper mine (Hamedan, Iran) was chosen as a polluted area where the amount of some heavy metals was several times higher than the natural soils. Flowers and young pods were removed from non-polluted and polluted plants, fixed in FAA 70, and subjected to developmental studies. Analysis of anther development in plants from contaminated sites showed general similarities in the pattern of pollen formation with those from non-polluted ones, but also deviation from typical form of major stages of anther and pollen development was seen in plants from polluted ones. Stabilizing of tapetum layer, increasing in tapetum layer numbers, thickening callose wall in the microspore mother cell stage, changing the anther shape, and decreasing the size of anther were the effects of heavy metals. Reduction of pollen number was also seen in the plants collected from polluted area.     

An in vitro study of the impact of 4mT static magnetic field to modify the differentiation rate of rat bone marrow stem cells into primordial germ cells

This investigation was performed to evaluate the differentiation capacity and alteration in genes expression patterns during in vitro differentiation of bone marrow stem cells into primordial germ cells using static magnetic field (4 mT) and BMP-4 (25 ng/ml). The rate of differentiation was investigated using the Real Time-PCR method for tracing expression of differentiation markers (Oct-4, Nanog, C-Myc, Fragilis, Mvh and Stella). Then, immunocytochemical reaction was carried out for detection of marker proteins (Oct4 and Mvh). Increasing of the exposure time of the 4 mT SMF (24 and 48 h) and treatment time with 25 ng/ml BMP4 (48 and 96 h) indicated a marked decrease in expression of pluripotency genes (Oct-4, Nanog and C-Myc) and Oct4 protein and increase in primordial germ cell-specific genes (Fragilis, Mvh and Stella) and Mvh protein compared with the control group. Final results showed that in a synergistic manner, the combination of SMF with BMP4 exaggerates the differentiation potential of BMSCs to PGCs by activating the MAPK pathway and altering the Ca²⁺ concentration.     

C17 prevents inflammatory arthritis and associated joint destruction in mice

C17 was first described about ten years ago as a gene expressed in CD34+ cells. A more recent study has suggested a role for C17 in chondrogenesis and development of cartilage. However, based on sequence analysis, we believe that C17 has homology to IL-2 and hence we present the hypothesis that C17 is a cytokine possessing immune-regulatory properties. We provide evidence that C17 is a secreted protein preferentially expressed in chondrocytes, hence in cartilage-rich tissues. Systemic expression of C17 in vivo reduces disease in a collagen antibody-induced arthritis model in mice (CAIA). Joint protection is evident by delayed disease onset, minimal edema, bone protection and absence of diverse histological features of disease. Expression of genes typically associated with acute joint inflammation and erosion of cartilage or bone is blunted in the presence of C17. Consistent with the observed reduction in bone erosion, we demonstrate reduced levels of RANKL in the paws and sera of mice over-expressing C17. Administration of C17 at the peak of disease, however, had no effect on disease progression, indicating that C17's immune-regulatory activity must be most prominent prior to or at the onset of severe joint inflammation. Based on this data we propose C17 as a cytokine that s contributes to immune homeostasis systemically or in a tissue-specific manner in the joint.