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.     

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.     

Effects of Short-Term Over-supplementation of Copper in Milk on Hematology,Serum Proteins,Weight Gain,and Health in Dairy Calves

Thirty-six calves were used in the present study. The animals were divided equally into three groups (control, test 1, and test 2). The three groups of calves were homogeneous for parity of dams, sex, and month of birth. From 14 days of age, in the test 1 group copper as copper sulfate (Merck Co, Germany) was added to each meal of milk at a rate of 10 mg/kg of milk for 14 days and in test 2 group copper as copper sulfate was added to each meal of milk at a rate of 20 mg/kg of milk for 14 days. Blood samples were taken by jugular venipuncture using disposable syringes at 14 (before Cu supplementation), 30, 60, and 80 days of age. Anticoagulated blood was used for CBC determination. Plane tubes were used for harvesting of serum and the amounts of total serum protein, albumin, iron, and copper were measured. Calves were weighted at birth and at the end of trial (day 80) and total gain and mean daily gain were calculated. Days of treatment for ill calves were also recorded during experiment. Group (treatment) had no significant effect on the amounts of measured parameters except MCH values (p < 0.05) which were significantly lower in test 1 group than other trial groups. Age (sampling time) had significant effects on the values of most measured parameters (p < 0.05) except WBC, lymphocyte, total protein, and fibrinogen. Significant interactions between sampling time and group were not seen for any of measured parameters. No significant differences were seen for total weight gain and mean daily gain between trial groups. Chi-square test revealed no significant difference for the days of treatment between trials groups.     

Reassessment of inclusion body-based production as a versatile opportunity for difficult-to-express recombinant proteins

The production of recombinant proteins in the microbial host Escherichia coli often results in the formation of cytoplasmic protein inclusion bodies (IBs). Proteins forming IBs are often branded as difficult-to-express, neglecting that IBs can be an opportunity for their production. IBs are resistant to proteolytic degradation and contain up to 90% pure recombinant protein, which does not interfere with the host metabolism. This is especially advantageous for host-toxic proteins like antimicrobial peptides (AMPs). IBs can be easily isolated by cell disruption followed by filtration and/or centrifugation, but conventional techniques for the recovery of soluble proteins from IBs are laborious. New approaches therefore simplify protein recovery by optimizing the production process conditions, and often include mild resolubilization methods that either increase the yield after refolding or avoid the necessity of refolding all together. For the AMP production, the IB-based approach is ideal, because these peptides often have simple structures and are easy to refold. The intentional IB production of almost every protein can be achieved by fusing recombinant proteins to pull-down tags. This review discusses the techniques available for IB-based protein production before considering technical approaches for the isolation of IBs from E. coli lysates followed by efficient protein resolubilization which ideally omits further refolding. The techniques are evaluated in terms of their suitability for the process-scale production and downstream processing of recombinant proteins and are discussed for AMP production as an example.     

Differential physiological and biochemical responses of Quercus infectoria and Q. libani to drought and charcoal disease

The vast oak-dominated forests of the Zagros Mountains in southwestern Iran currently undergo large-scale dieback driven by a combination of drought and increasing incidence of charcoal disease caused by the fungal pathogens Biscogniauxia mediterranea and Obolarina persica. Here, we explore the interactive effects between drought and charcoal disease agents on the physiology and biochemistry of Quercus infectoria and Quercus libani seedlings. The combination of pathogen attack and water limitation hampered plant development, especially in Q. libani seedlings, negatively affecting growth, biomass production, photosynthetic efficiency, and leaf water potential. An increase in markers of oxidative damage together with the upregulation of the antioxidant defense revealed that drought stress and pathogen infection led to pro-oxidative conditions in both oak species, especially in Q. libani, where larger changes in malondialdehyde and hydrogen peroxide occurred. The upregulation of the antioxidant system was more prominent in Q. infectoria than in Q. libani, resulting in enhanced enzyme activity and accumulation of non-enzymatic antioxidants. Fungal infection stimulated the activity of chitinase, phenylalanine ammonia lyase and β-1,3-glucanase in Q. infectoria leaves and this response became more pronounced under water shortage. Our study highlights that drought stress greatly intensifies the effects of the charcoal disease. Moreover, our findings imply superior stress resistance of Q. infectoria conferred by a highly efficient antioxidant system, strong osmotic adjustment (through proline), and increases in resistance enzymes and secondary metabolites (phenols and flavonoids). Future investigations should focus on adult trees in their natural habitat including interactions with soil factors and other pathogens like nematodes, bacteria and other fungi. Because the present research was conducted on oak seedlings, the findings can be considered by forest nursery managers.     

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.