Detection of Bacillus thuringiensis genes in transgenic maize by the PCR method and FTA paper technology

We optimized the PCR method to detect genetically engineered Bacillus thuringiensis (Bt) maize in open quarantine fields in Kenya. Many factors affect the extraction of the DNA from plants, such as the amount of tissue available, the condition of the plant material, the numbers of steps involved in the extraction procedure, and the required purity needed. We tested the application of the FTA paper technology for field sampling whereby leaf materials are not removed and transported from the site. We also applied the PCR method, a technique that is widely used for detection of genetically modified organism (GMOs). We used primers specific to the Bt genes present in the transgenic maize to screen for the Bt genes Cry 1Ab and Cry 1Ba

Screening tropical maize lines for the production and regeneration of friable and embryogenic type II callus

Twenty two maize lines popularly used by breeders in the Kenyan maize program were screened for their ability to form type II callus. The immature embryos were harvested two weeks after pollination. Two highland lines showed high embryogenic response and formed friable, type II calli. While 16 lines screened showed poor or retarded growth with subsequent death. There was successful plant regeneration from four lines collected from the highland breeding program that are genetically related. The results suggested that genetic factors may be responsible for the differences seen in the regenerability of the tropical lines. The two lines CMB7 and CMB8 are considered suitable for further evaluation using a transformation syste

Optimization of FTA technology for large scale plant DNA isolation for use in marker assisted selection

Conventional methods for DNA acquisition and storage require expensive reagents and equipments. Experimental fields located in remote areas and large sample size presents greater challenge to developing country institutions constrained financially. FTATM technology uses a single format utilizing basic tools found in laboratory. In this study, FTATM cards were used to collect over 3000 samples from a field located 130 km and used to screen progeny plants using PCR-marker-assisted selection. PCR product yields and quality are sufficient for reliable scoring, distinguishing heterozygous fromhomozygous plants using ABI 3730 sequencer. Results indicate that this method is faster, easier and in-expensive

Marker assisted introgression of opaque2 gene into herbicide resistant elite maize inbred lines

Marker assisted selection in combination with conventional breeding can greatly accelerate the introgression of modified opaque2 genotype into herbicide resistant maize. By combining these two approaches, time and costs are greatly minimized. The application of opaque2 allele specific SSR markers was done on materials already undergoing selection in a breeding program for converting herbicide resistant maize lines into quality protein maize (QPM) which is the equivalent of modified opaque2 phenotype. The breeder had selected QPM lines using the light table in the previous cycle and we used leaf samples to extract DNA for analysis of the presence of the opaque2 gene using SSR markers. Two co-dominant SSR markers phi057 and umc1066 and a dominant marker phi112 were used. Umc1216, a modifier marker was also tested in combination with the opaque2 markers with theobjective of using the marker to select for modifiers for the opaque2 phenotype. The modified FTA paper technology protocol was applied in field sampling. The results showed 97% of the lines wereopaque2 while 3% were non-opaque2. Both methods of conventional breeding using light table and marker assisted selection (MAS) were comparable. However, the application of SSR markers and theFTA technology offers the breeder a fast, time saving, reliable and less labour intensive method of screening QPM maize during the early growing stages instead of having to wait to screen the kernels onthe light table after harvesting. Moreover, the routine biochemical analysis for high lysine and tryptophan levels need not be carried out at each backcross since the presence of the opaque2 gene is confirmed with markers

Phase I dose escalation and pharmacokinetic study of pluronic polymer-bound doxorubicin (SP1049C) in patients with advanced cancer

SP1049C is a novel anticancer agent containing doxorubicin and two nonionic pluronic block copolymers. In preclinical studies, SP1049C demonstrated increased efficacy compared to doxorubicin. The objectives of this first phase I study were to determine the toxicity profile, dose-limiting toxicity, maximum tolerated dose and pharmacokinetic profile of SP1049C, and to document any antitumour activity. The starting dose was 5 mg m−2 (doxorubicin content) as an intravenous infusion once every 3 weeks for up to six cycles. A total of 26 patients received 78 courses at seven dose levels. The dose-limiting toxicity was myelosuppression and DLT was reached at 90 mg m−2. The maximum tolerated dose was 70 mg m−2 and is recommended for future trials. The pharmacokinetic profile of SP1049C showed a slower clearance than has been reported for conventional doxorubicin. Evidence of antitumour activity was seen in some patients with advanced resistant solid tumours. Phase II trials with this agent are now warranted to further define its antitumour activity and safety profile

Sorafenib in advanced melanoma: a Phase II randomised discontinuation trial analysis

The effects of sorafenib – an oral multikinase inhibitor targeting the tumour and tumour vasculature – were evaluated in patients with advanced melanoma enrolled in a large multidisease Phase II randomised discontinuation trial (RDT). Enrolled patients received a 12-week run-in of sorafenib 400 mg twice daily (b.i.d.). Patients with changes in bi-dimensional tumour measurements <25% from baseline were then randomised to sorafenib or placebo for a further 12 weeks (ie to week 24). Patients with ⩾25% tumour shrinkage after the run-in continued on open-label sorafenib, whereas those with ⩾25% tumour growth discontinued treatment. This analysis focussed on secondary RDT end points: changes in bi-dimensional tumour measurements from baseline after 12 weeks and overall tumour responses (WHO criteria) at week 24, progression-free survival (PFS), safety and biomarkers (BRAF, KRAS and NRAS mutational status). Of 37 melanoma patients treated during the run-in phase, 34 were evaluable for response: one had ⩾25% tumour shrinkage and remained on open-label sorafenib; six (16%) had <25% tumour growth and were randomised (placebo, n=3; sorafenib, n=3); and 27 had ⩾25% tumour growth and discontinued. All three randomised sorafenib patients progressed by week 24; one remained on sorafenib for symptomatic relief. All three placebo patients progressed by week-24 and were re-started on sorafenib; one experienced disease re-stabilisation. Overall, the confirmed best responses for each of the 37 melanoma patients who received sorafenib were 19% stable disease (SD) (ie n=1 open-label; n=6 randomised), 62% (n=23) progressive disease (PD) and 19% (n=7) unevaluable. The overall median PFS was 11 weeks. The six randomised patients with SD had overall PFS values ranging from 16 to 34 weeks. The most common drug-related adverse events were dermatological (eg rash/desquamation, 51%; hand-foot skin reaction, 35%). There was no relationship between V600E BRAF status and disease stability. DNA was extracted from the biopsies of 17/22 patients. Six had V600E-positive tumours (n=4 had PD; n=1 had SD; n=1 unevaluable for response), and 11 had tumours containing wild-type BRAF (n=9 PD; n=1 SD; n=1 unevaluable for response). In conclusion, sorafenib is well tolerated but has little or no antitumour activity in advanced melanoma patients as a single agent at the dose evaluated (400 mg b.i.d.). Ongoing trials in advanced melanoma are evaluating sorafenib combination therapies

The Adaptor Molecule Nck Localizes the WAVE Complex to Promote Actin Polymerization during CEACAM3-Mediated Phagocytosis of Bacteria

Background: CEACAM3 is a granulocyte receptor mediating the opsonin-independent recognition and phagocytosis of human-restricted CEACAM-binding bacteria. CEACAM3 function depends on an intracellular immunoreceptor tyrosine-based activation motif (ITAM)-like sequence that is tyrosine phosphorylated by Src family kinases upon receptor engagement. The phosphorylated ITAM-like sequence triggers GTP-loading of Rac by directly associating with the guanine nucleotide exchange factor (GEF) Vav. Rac stimulation in turn is critical for actin cytoskeleton rearrangements that generate lamellipodial protrusions and lead to bacterial uptake. Principal Findings: In our present study we provide biochemical and microscopic evidence that the adaptor proteins Nck1 and Nck2, but not CrkL, Grb2 or SLP-76, bind to tyrosine phosphorylated CEACAM3. The association is phosphorylation-dependent and requires the Nck SH2 domain. Overexpression of the isolated Nck1 SH2 domain, RNAi-mediated knock-down of Nck1, or genetic deletion of Nck1 and Nck2 interfere with CEACAM3-mediated bacterial internalization and with the formation of lamellipodial protrusions. Nck is constitutively associated with WAVE2 and directs the actin nucleation promoting WAVE complex to tyrosine phosphorylated CEACAM3. In turn, dominant-negative WAVE2 as well as shRNA-mediated knock-down of WAVE2 or the WAVE-complex component Nap1 reduce internalization of bacteria. Conclusions: Our results provide novel mechanistic insight into CEACAM3-initiated phagocytosis. We suggest that the CEACAM3 ITAM-like sequence is optimized to co-ordinate a minimal set of cellular factors needed to efficiently trigger actin-based lamellipodial protrusions and rapid pathogen engulfment

Reconstruction of metabolic pathways for the cattle genome

<p>Abstract</p> <p>Background</p> <p>Metabolic reconstruction of microbial, plant and animal genomes is a necessary step toward understanding the evolutionary origins of metabolism and species-specific adaptive traits. The aims of this study were to reconstruct conserved metabolic pathways in the cattle genome and to identify metabolic pathways with missing genes and proteins. The MetaCyc database and PathwayTools software suite were chosen for this work because they are widely used and easy to implement.</p> <p>Results</p> <p>An amalgamated cattle genome database was created using the NCBI and Ensembl cattle genome databases (based on build 3.1) as data sources. PathwayTools was used to create a cattle-specific pathway genome database, which was followed by comprehensive manual curation for the reconstruction of metabolic pathways. The curated database, CattleCyc 1.0, consists of 217 metabolic pathways. A total of 64 mammalian-specific metabolic pathways were modified from the reference pathways in MetaCyc, and two pathways previously identified but missing from MetaCyc were added. Comparative analysis of metabolic pathways revealed the absence of mammalian genes for 22 metabolic enzymes whose activity was reported in the literature. We also identified six human metabolic protein-coding genes for which the cattle ortholog is missing from the sequence assembly.</p> <p>Conclusion</p> <p>CattleCyc is a powerful tool for understanding the biology of ruminants and other cetartiodactyl species. In addition, the approach used to develop CattleCyc provides a framework for the metabolic reconstruction of other newly sequenced mammalian genomes. It is clear that metabolic pathway analysis strongly reflects the quality of the underlying genome annotations. Thus, having well-annotated genomes from many mammalian species hosted in BioCyc will facilitate the comparative analysis of metabolic pathways among different species and a systems approach to comparative physiology.</p

MicroMotility: State of the art, recent accomplishments and perspectives on the mathematical modeling of bio-motility at microscopic scales

Mathematical modeling and quantitative study of biological motility (in particular, of motility at microscopic scales) is producing new biophysical insight and is offering opportunities for new discoveries at the level of both fundamental science and technology. These range from the explanation of how complex behavior at the level of a single organism emerges from body architecture, to the understanding of collective phenomena in groups of organisms and tissues, and of how these forms of swarm intelligence can be controlled and harnessed in engineering applications, to the elucidation of processes of fundamental biological relevance at the cellular and sub-cellular level. In this paper, some of the most exciting new developments in the fields of locomotion of unicellular organisms, of soft adhesive locomotion across scales, of the study of pore translocation properties of knotted DNA, of the development of synthetic active solid sheets, of the mechanics of the unjamming transition in dense cell collectives, of the mechanics of cell sheet folding in volvocalean algae, and of the self-propulsion of topological defects in active matter are discussed. For each of these topics, we provide a brief state of the art, an example of recent achievements, and some directions for future research