Novel biotechnology approaches in colorectal cancer diagnosis and therapy

With ever-increasing molecular information about colorectal cancer (CRC), there is an expectation to detect more sensitive and specific molecular markers for new advanced diagnostic methods that can surpass the limitations of current screening tests. Moreover, enhanced molecular pathology knowledge about cancer has led to the development of targeted therapies, designed to interfere with specific aberrant biological pathways in cancer. Furthermore, biotechnology has opened a new window in CRC diagnosis and treatment by introducing different application of antibodies, antibody fragments, non-Ig scaffold proteins, and aptamers in targeted therapy and drug delivery. This review summarizes the molecular diagnostic and therapeutic approaches in CRC with a focus on genetic and epigenetic alterations, protein and metabolite markers as well as targeted therapy and drug delivery by Ig-scaffold proteins, non-Ig scaffold proteins, nanobodies, and aptamers.     

Serum Zinc and Copper Levels in Ischemic Cardiomyopathy

Changes in the copper (Cu) and zinc (Zn) concentrations have been reported previously in ischemic cardiomyopathy (ISCMP). Due to controversial results, the aims of this study were to compare levels of Cu, Zn, and Zn/Cu ratio of ISCMP patients with healthy volunteers and also to investigate the possible relationship between trace elements status in ISCMP patients with the severity of clinical disease based on the New York Heart Association (NYHA) classification. The subjects of this study consisted of 30 ISCMP and 27 healthy volunteers. ISCMP was diagnosed with a history of previous myocardial infarction and also coronary artery disease was confirmed by coronary angiography. Exclusion criteria were renal or hepatic insufficiency, alcohol usage, and intake of supplements containing Cu or Zn within 1 week. Cu and Zn levels have been assayed with atomic absorption spectrophotometry. Statistical analysis was performed with the SPSS 10 software using independent sample t test for comparing the levels of Cu and Zn between ISCMP and normal subjects. The mean Cu level of the ISCMP group (1.54 ± 0.52 mg/L) was significantly more than the Cu levels of the healthy volunteers (1.31 ± 0.24 mg/L; p = 0.048). The mean Zn levels of the ISCMP and healthy volunteers were 1.05 ± 0.28 and 1.12 ± 0.42, respectively, without any significant difference between groups. There was a trend for higher Cu level, lower Zn level, and lower Zn/Cu ratio in NYHA III patients in comparison with NYHA II group. Considering the results of this study, Cu may have a role in the development of ISCMP. Interventions such as administration of Cu chelators to relieve the symptoms or to decrease the progression of ISCMP is needed to be examined in large clinical trials. In this study, the Zn level of ISCMP patients was not significantly different in comparison with the healthy volunteers.     

Decreasing the immunogenicity of arginine deiminase enzyme via structure‐based computational analysis

The clinical applications of therapeutic enzymes are often limited due to their immunogenicity. B-cell epitope removal is an effective approach to solve this obstacle. The identification of hot spot epitopic residues is a critical step in the removal of protein B-cell epitope. Hereof, computational approaches are a suitable alternative to costly and labor-intensive experimental approaches. Arginine deiminase, a Mycoplasma arginine-catabolizing enzyme, is in the clinical trial for treating arginine auxotrophic cancers, especially hepatocellular carcinomas and melanomas through depleting plasma arginine and causing cell starvation. In this study, arginine deiminase from Mycoplasma hominis (MhADI) was computationally analyzed for recognizing and locating its immune-reactive regions. The 3D structure of the bioactive form of MhADI was modeled. The B-cell epitope mapping of protein was performed using various servers with different algorithms. Six segments: 31–40, 48–55, 131–140, 196–206, 294–314, and 331–344 were predicted to be the consensus immunogenic regions. The modification of epitopic hot spot residue was performed to reduce immune-reactiveness. The hot spot residue was selected considering a high B-cell epitope score, convexity index, surface accessibility, flexibility, and hydrophilicity. The structure stability of native and mutant proteins was evaluated through molecular dynamics simulation. The E304L mutein was suggested as a lower antigenic and stable enzyme derivative.     

The Association of Physical and Environmental Factors with Abundance and Distribution Patterns of Groupers around Kolombangara Island, Solomon Islands

I collected baseline abundance data on groupers from the reefs of Vavanga village on Kolombangara Island, Solomon Islands. Physical and environmental factors significantly affected the abundance and distribution patterns of groupers. Size and age distribution of groupers varied with depth. Power analysis on the abundance data showed that although power could be calculated to within an acceptable level from a management perspective for abundant species such as the coral hind, Cephalopholis miniata, the same could not be done for larger and naturally scarce species, such as the humpback grouper, Cromileptes altivelis.     

Scaring Nemo: Contrasting effects of observer presence on two anemonefish species

Behaviours of Clark's anemonefish Amphiprion clarkii and the dusky anemonefish Amphiprion melanopus were studied in Vanuatu. Six anemones and their resident fish were observed for typical behaviours (hiding, watching, roaming, inter-, and intraspecific behaviour) with and without the presence of a snorkelling observer. Observer presence had significant but contrasting effects on hiding behaviour in A. clarkii and A. melanopus. Bolder anemonefish species may be able to outcompete other species in areas with high human presence.     

DNA Detection Based on Localized Surface Plasmon Resonance Spectroscopy of Ag@Au Biocomposite Nanoparticles

Noble metal nanoparticles (NPs) have attracted much attention due to their unique physical and chemical properties such as tunable surface plasmonics, high-efficiency electrochemical sensing, and enhanced fluorescence. We produced two biosensor chips consisting of Ag@Au bimetallic nanoparticles (BNPs) on a carbon thin film by simple RF-sputtering and RF-plasma-enhanced chemical vapor co-deposition. We deposited Au NPs with average size of 4 nm (Au₁ NPs) or 11 nm (Au₂ NPs) on a sensor chip consisting of Ag NPs with mean size of 15 nm, and we investigated the effect of shell size (Au NPs) on the chemical activities of the resulting Ag@Au₁ BNPs and Ag@Au₂ BNPs. We estimated the average size and morphology of Ag@Au BNPs by scanning electron microscopy (SEM) and atomic force microscopy (AFM) images. X-ray diffraction (XRD) patterns revealed that Ag NPs and Au NPs had face-centered cubic (FCC) structure. We studied aging of the biosensor chips consisting of Ag@Au BNPs by localized surface plasmon resonance (LSPR) spectroscopy for up to 3 months. UV–visible aging of the prepared samples indicated that Ag@Au₁ BNPs, which corresponded to Ag NPs covered with smaller Au NPs, were more chemically active than Ag@Au₂ BNPs. Furthermore, we evaluated changes in the LSPR absorption peaks of Ag@Au₁ BNPs and bare Ag NPs in the presence of a DNA primer decamer at fM concentrations, to find that Ag@Au₁ BNPs were more sensitive biosensor chips within a short response time as compared to bare Ag NPs.

     

Neuronal XBP-1 Activates Intestinal Lysosomes to Improve Proteostasis in C. elegans

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The Intensity of a Bean Fusarium Root Rot Epidemic is Dependent on Planting Strategies

Restricting Fusarium root rot (FRR) epidemics and improving productivity using fewer chemicals is a major concern in bean‐growing regions. The main purpose of this research was to identify the planting strategies associated with FRR development and seed production in bean crops. A 2‐year study of 122 commercial bean farms in four major producing regions in Zanjan, Iran, was performed to characterize the associations of farming indicators with FRR and productivity. Linear mixed‐effect models, contingency tables and correspondence analyses were used to describe the variables relationships. Low disease and high productivity were linked to herbicide and manure applications, fungicidal treatment of seeds, manual sowing and sprinkler irrigation. Furrow irrigation, mechanical sowing, planting on raised seedbeds, the lack of fertilizer and herbicide use accounted for high disease and low seed production. The results of the study provide further evidence of factors contributions to the wider FRR spread over bean‐cropping systems. Overall, this suggests that the selected composition of planting strategies can improve bean production and reduce FRR intensity.     

Epigenetic Modification of MicroRNA-219-1 and Its Association with Glioblastoma Multiforme

Biochemistry (Moscow) - MicroRNA-219-1 (miR-219-1) acts as a tumor suppressor in a variety of cancers but, the regulatory epigenetic mechanism involved in its gene expression level has not been...