Single-chain antibody fragments: Purification methodologies

At present, single-chain variable fragments (scFv) of antibodies are considered one of the most important tools in human therapies. Wide applications of antibodies are being exploited in different medical, pharmaceutical and research areas. These molecules maintain the same binding functionality that full length antibodies but possess several advantageous features as quickness to penetrate the tissues, easy manipulation, fast elimination of their immunocomplex and the possibility of being produced in simple expression systems like bacteria and yeast. The increasing demand in antibody based methodologies is driving advances in the production and purification of genetically engineered antibodies and antibody fragments. While advances in expression systems allow the production of high titers of antibodies, there exist some limits imposed by the downstream methodologies which are not efficient enough to ensure their industrialization.The main aim of this review is to highlight the principal characteristics of single-chain variable fragments of antibodies addressing advances and perspectives on scFv purification.     

Blood Perfusion in a Murine Fibrosarcoma Tumor Model After Direct Current Electrotherapy a Study with 86Rb Extraction Technique

Electrotherapy with low-level direct current (DC) can induce antitu-mor effects in various tumor models. Applied in combination with certain anticancer drugs, it can significantly increase their effectiveness. It has been suggested that the demonstrated effects of electrotherapy arise from its modification of tumor blood flow. The effect of such treatment on blood perfusion of solid subcutaneous Sa-1 fibrosarcoma tumors in A/J mice was investigated with a ⁸⁶rubidium extraction technique. Following electrotherapy, the relative tissue perfusion of tumors was decreased by more than 50%. Three days after treatment, partial reperfusion of tumors occurred. The dynamics of the perfusion changes induced by electrotherapy are in agreement with tumor growth dynamics following this procedure. The effect of electrotherapy on the blood supply of tumors may be the major mechanism of antitumor action in our model. Electrotherapy could be useful as an adjuvant local procedure to other treatment modalities that require a hypoxic environment for their effectiveness.     

MEK2 regulates ribonucleotide reductase activity through functional interaction with ribonucleotide reductase small subunit p53R2

The p53R2 protein, a newly identified member of the ribonucleotide reductase family that provides nucleotides for DNA damage repair, is directly regulated by p53. We show that p53R2 is also regulated by a MEK2 (ERK kinase 2/MAP kinase kinase 2)-dependent pathway. Increased MEK1/2 phosphorylation by serum stimulation coincided with an increase in the RNR activity in U2OS and H1299 cells. The inhibition of MEK2 activity, either by treatment with a MEK inhibitor or by transfection with MEK2 siRNA, dramatically decreased the serum-stimulated RNR activity. Moreover, p53R2 siRNA, but not R2 siRNA, significantly inhibits serum-stimulated RNR activity, indicating that p53R2 is specifically regulated by a MEK2-dependent pathway. Co-immunoprecipitation analyses revealed that the MEK2 segment comprising amino acids 65–171 is critical for p53R2–MEK2 interaction, and the binding domain of MEK2 is required for MEK2-mediated increased RNR activity. Phosphorylation of MEK1/2 was greatly augmented by ionizing radiation, and RNR activity was concurrently increased. Ionizing radiation-induced RNR activity was markedly attenuated by transfection of MEK2 or p53R2 siRNA, but not R2 siRNA. These data show that MEK2 is an endogenous regulator of p53R2 and suggest that MEK2 may associate with p53R2 and upregulate its activity.     

Controversial aspects of oncogene-induced senescence

Oncogene-induced senescence (OIS) is a fail-safe mechanism that is developed to suppress cell proliferation caused by aberrant activation of oncoproteins in normal cells. Most of the available literature considers senescence to be caused by activated RAS or RAF proteins. In the current review, we will discuss some of the controversial aspects of RAS- or RAF-induced senescence in different types of normal cells: are tumor suppressors important for OIS? What is the role of DNA damage in OIS? Are there different types of OIS?     

A Murine Model of Subarachnoid Hemorrhage

In this video publication a standardized mouse model of subarachnoid hemorrhage (SAH) is presented. Bleeding is induced by endovascular Circle of Willis perforation (CWp) and proven by intracranial pressure (ICP) monitoring. Thereby a homogenous blood distribution in subarachnoid spaces surrounding the arterial circulation and cerebellar fissures is achieved. Animal physiology is maintained by intubation, mechanical ventilation, and continuous on-line monitoring of various physiological and cardiovascular parameters: body temperature, systemic blood pressure, heart rate, and hemoglobin saturation. Thereby the cerebral perfusion pressure can be tightly monitored resulting in a less variable volume of extravasated blood. This allows a better standardization of endovascular filament perforation in mice and makes the whole model highly reproducible. Thus it is readily available for pharmacological and pathophysiological studies in wild type and genetically altered mice.     

Modification of plant bait technique for direct diagnosis for Rhizoctonia rice pathogens from Myanmar paddy field soils

A modified baiting technique was conducted for selective isolation, fungal DNA diagnosis and fungal cell lipid assay derived from Myanmar isolates of Rhizoctonia spp., causal agents of rice sheath diseases by trapping selective plant stem segments. Bait plant materials of rice, mat rush and cotton were successfully used to isolate R. solani AG1-IA, R. oryzae and R. oryzae-sativae. Moreover, the three plant materials were also effectively used to detect genomic DNA derived from all Rhizoctonia spp. obtained from Myanmar. Rice segment was the most successful materials for detection of fungal cell lipids including palmitic, stearic and linoleic acids. The results of this experiment demonstrate that bait plant materials of rice, mat rush and cotton were the best useful tools for not only direct isolation, but also fungal DNA diagnosis and cell lipid assay of Myanmar soil environmental conditions.     

Gene silencing in Escherichia coli using antisense RNAs expressed from doxycycline‐inducible vectors

Here, we report on the construction of doxycycline (tetracycline analogue)‐inducible vectors that express antisense RNAs in Escherichia coli. Using these vectors, the expression of genes of interest can be silenced conditionally. The expression of antisense RNAs from the vectors was more tightly regulated than the previously constructed isopropyl‐β‐D‐galactopyranoside‐inducible vectors. Furthermore, expression levels of antisense RNAs were enhanced by combining the doxycycline‐inducible promoter with the T7 promoter‐T7 RNA polymerase system; the T7 RNA polymerase gene, under control of the doxycycline‐inducible promoter, was integrated into the lacZ locus of the genome without leaving any antibiotic marker. These vectors are useful for investigating gene functions or altering cell phenotypes for biotechnological and industrial applications.

Significance and Impact of the Study

A gene silencing method using antisense RNAs in Escherichia coli is described, which facilitates the investigation of bacterial gene function. In particular, the method is suitable for comprehensive analyses or phenotypic analyses of genes essential for growth. Here, we describe expansion of vector variations for expressing antisense RNAs, allowing choice of a vector appropriate for the target genes or experimental purpose.     

Integrated control of apple pests in New Zealand

A technique is described whereby 5th‐instar larvae of the codling moth (Laspeyresia pomonella) which have finished feeding can be tagged externally with cobalt‐58 and released on apple trees, where they seek cocooning sites. Two μCi ⁵⁸Co per insect did not significantly affect larval survival in the field, or subsequent pupation, emergence, mating, and oviposition in the laboratory. Tagging was more efficient than whole‐tree scraping for the location of cocoons, and was non‐destructive of both the insects and their cocooning sites.

Relocation and observation of the tagged larvae in their cocoons permitted accurate estimation of mortality from when they left the fruit (= release) until adult emergence in the following spring. Natural mortality of larvae seeking cocooning sites was attributed mainly to insect predators, and varied significantly between trees and blocks, averaging 57% over 6 years. Avian predation by the silvereye (Zosterops lateralis) was the greatest hazard to cocooned larvae; this, too, varied significantly between blocks, and averaged 53% over the same period. Both mortalities appeared to be density‐related.     

Crystal structure of the invertebrate bifunctional purine biosynthesis enzyme PAICS at 2.8 Å resolution

Two important steps of the de novo purine biosynthesis pathway are catalyzed by the 5‐aminoimidazole ribonucleotide carboxylase and the 4‐(N‐succinylcarboxamide)‐5‐aminoimidazole ribonucleotide synthetase enzymes. In most eukaryotic organisms, these two activities are present in the bifunctional enzyme complex known as PAICS. We have determined the 2.8‐Å resolution crystal structure of the 350‐kDa invertebrate PAICS from insect cells (Trichoplusia ni) using single‐wavelength anomalous dispersion methods. Comparison of insect PAICS to human and prokaryotic homologs provides insights into substrate binding and reveals a highly conserved enzymatic framework across divergent species. Proteins 2013; 81:1473–1478. © 2013 Wiley Periodicals, Inc.     

The design of a peptide sequence to inhibit HIV replication: a search algorithm combining Monte Carlo and self-consistent mean field techniques

We developed a search algorithm combining Monte Carlo (MC) and self-consistent mean field techniques to evolve a peptide sequence that has good binding capability to the anticodon stem and loop (ASL) of human lysine tRNA species, tRNA^Lys3, with the ultimate purpose of breaking the replication cycle of human immunodeficiency virus-1. The starting point is the 15-amino-acid sequence, RVTHHAFLGAHRTVG, found experimentally by Agris and co-workers to bind selectively to hypermodified tRNA^Lys3. The peptide backbone conformation is determined via atomistic simulation of the peptide-ASL^Lys3 complex and then held fixed throughout the search. The proportion of amino acids of various types (hydrophobic, polar, charged, etc.) is varied to mimic different peptide hydration properties. Three different sets of hydration properties were examined in the search algorithm to see how this affects evolution to the best-binding peptide sequences. Certain amino acids are commonly found at fixed sites for all three hydration states, some necessary for binding affinity and some necessary for binding specificity. Analysis of the binding structure and the various contributions to the binding energy shows that: 1) two hydrophilic residues (asparagine at site 11 and the cysteine at site 12) “recognize” the ASL^Lys3 due to the VDW energy, and thereby contribute to its binding specificity and 2) the positively charged arginines at sites 4 and 13 preferentially attract the negatively charged sugar rings and the phosphate linkages, and thereby contribute to the binding affinity.