Development of Agriculture Biotechnology in Pakistan

Agriculture plays an important role in the national economy of Pakistan, where most of the rapidly increasing population resides in rural areas and depends on agriculture for subsistence. Biotechnology has considerable potential for promoting the efficiency of crop improvement, food production, and poverty reduction. Use of modern biotechnology started in Pakistan since 1985. Currently, there are 29 biotech centers/institutes in the country. However, few centers have appropriate physical facilities and trained manpower to develop genetically modified (GM) crops. Most of the activities have been on rice and cotton, which are among the top 5 crops of Pakistan. Biotic (virus/bacterial/insect) and abiotic (salt) resistant and quality (male sterility) genes have already been incorporated in some crop plants. Despite acquiring capacity to produce transgenic plants, no GM crops, either produced locally or imported, have been released in the country. Pakistan is signatory to the World Trade Organization, Convention on Biological Diversity, and Cartagena protocols. Several legislations under the Agreement on Trade-Related Aspects of Intellectual Property Rights have been promulgated in the country. National Biosafety Guidelines have been promulgated in April 2005. The Plant Breeders Rights Act, Amendment in Seed Act-1976, and Geographical Indication for Goods are still passing through discussion, evaluation, and analysis phases. Meanwhile, an illegal GM crop (cotton) has already sneaked into farmer's field. Concerted and coordinated efforts are needed among various ministries for implementation of regulation and capacity building for import/export and local handling of GM crops. Pakistan could easily benefit from the experience of Asian countries, especially China and India, where conditions are similar and the agriculture sector is almost like that of Pakistan. Thus, the exchange of information and experiences is important among these nations.

Aflatoxin Contamination of Milk Marketed in Pakistan: A Longitudinal Study

A longitudinal one-year study was conducted to determine aflatoxin M₁ levels in different types of milk marketed in Pakistan. Processed and raw liquid milk from 21 sources, two milk powder and six tea whitener brands were sampled on monthly basis from Islamabad. The aflatoxin M₁ levels in liquid milk were lower (p < 0.05) in summer (April to July) compared with the levels in winter (January, November and December). The mean aflatoxin M₁ levels were 254.9, 939.5, and 1535.0 ng/L in UHT, pasteurized, and raw milk, respectively (differing at p < 0.001). The mean toxin level in powdered milk after reconstitution was 522.1 ng/L. Overall, 12.9, 41.0, 91.9 and 50.0% of the UHT, pasteurized, raw and powdered milk samples, respectively, exceeded the Codex maximum tolerable limit of 500 ng of aflatoxin M₁/L. It was estimated that consumers of raw and processed milk were exposed to 11.9 and 4.5 ng aflatoxin M₁, respectively, per kg of body weight daily. The study indicates potential aflatoxin M₁ exposure risks for the consumers of raw milk in the country. The levels of the toxin though comparatively lower in milk powder, requires attention as this type of milk is consumed by infants.

Co-expression of YieF and PhoN in Deinococcus radiodurans R1 improves uranium bioprecipitation by reducing chromium interference

Overexpression of the enzyme phosphatase (PhoN/PhoK) in the radiation-resistant bacterium Deinococcus radiodurans could be an efficient strategy for uranium remediation. However, the presence of other metals in nuclear wastes often interferes with uranium bioprecipitation. In our study, the uranium-precipitating ability of the PhoN-expressing D. radiodurans strain (Deino-phoN) significantly decreased by 45.4% in 13 h in the presence of chromium (VI); however, it was partially recovered after supplementation with chromium (III). Therefore, the reduction of chromium (VI) to chromium (III) was obtained by the co-expression of the YieF protein and PhoN in D. radiodurans (Deino-phoN-yieF). As a result, an increase in the chromium (VI) reduction (25.1%) rate was observed in 24 h. Furthermore, uranium precipitation also increased by 28.0%. For the decontamination of groundwater, we immobilized Deino-phoN-yieF cells using Polyvinyl alcohol (PVA)-sodium alginate (SA) beads, followed by incubation in a bioreactor. Approximately 99% of chromium (VI) and uranium (VI) was removed after 4 continuous cycles operated for a period of over 20 days at room temperature (25 °C). Therefore, Deino-phoN-yieF could be used as a potential biological agent for mixed radioactive nuclear waste remediation.

Genetics and Genomics of Cotton Leaf Curl Disease, Its Viral Causal Agents and Whitefly Vector: A Way Forward to Sustain Cotton Fiber Security

Cotton leaf curl disease (CLCuD) after its first epidemic in 1912 in Nigeria, has spread to different cotton growing countries including United States, Pakistan, India, and China. The disease is of viral origin-transmitted by the whitefly Bemisia tabaci, which is difficult to control because of the prevalence of multiple virulent viral strains or related species. The problem is further complicated as the CLCuD causing virus complex has a higher recombination rate. The availability of alternate host crops like tomato, okra, etc., and practicing mixed type farming system have further exaggerated the situation by adding synergy to the evolution of new viral strains and vectors. Efforts to control this disease using host plant resistance remained successful using two gene based-resistance that was broken by the evolution of new resistance breaking strain called Burewala virus. Development of transgenic cotton using both pathogen and non-pathogenic derived approaches are in progress. In future, screening for new forms of host resistance, use of DNA markers for the rapid incorporation of resistance into adapted cultivars overlaid with transgenics and using genome editing by CRISPR/Cas system would be instrumental in adding multiple layers of defense to control the disease-thus cotton fiber production will be sustained.

DNA barcoding of Bemisia tabaci complex (Hemiptera: Aleyrodidae) reveals southerly expansion of the dominant whitefly species on cotton in Pakistan

BACKGROUND

Although whiteflies (Bemisia tabaci complex) are an important pest of cotton in Pakistan, its taxonomic diversity is poorly understood. As DNA barcoding is an effective tool for resolving species complexes and analyzing species distributions, we used this approach to analyze genetic diversity in the B. tabaci complex and map the distribution of B. tabaci lineages in cotton growing areas of Pakistan.

METHODS/PRINCIPAL FINDINGS

Sequence diversity in the DNA barcode region (mtCOI-5') was examined in 593 whiteflies from Pakistan to determine the number of whitefly species and their distributions in the cotton-growing areas of Punjab and Sindh provinces. These new records were integrated with another 173 barcode sequences for B. tabaci, most from India, to better understand regional whitefly diversity. The Barcode Index Number (BIN) System assigned the 766 sequences to 15 BINs, including nine from Pakistan. Representative specimens of each Pakistan BIN were analyzed for mtCOI-3' to allow their assignment to one of the putative species in the B. tabaci complex recognized on the basis of sequence variation in this gene region. This analysis revealed the presence of Asia II 1, Middle East-Asia Minor 1, Asia 1, Asia II 5, Asia II 7, and a new lineage "Pakistan". The first two taxa were found in both Punjab and Sindh, but Asia 1 was only detected in Sindh, while Asia II 5, Asia II 7 and "Pakistan" were only present in Punjab. The haplotype networks showed that most haplotypes of Asia II 1, a species implicated in transmission of the cotton leaf curl virus, occurred in both India and Pakistan.

CONCLUSIONS

DNA barcodes successfully discriminated cryptic species in B. tabaci complex. The dominant haplotypes in the B. tabaci complex were shared by India and Pakistan. Asia II 1 was previously restricted to Punjab, but is now the dominant lineage in southern Sindh; its southward spread may have serious implications for cotton plantations in this region.

Analyzing mosquito (Diptera: culicidae) diversity in Pakistan by DNA barcoding

BACKGROUND

Although they are important disease vectors mosquito biodiversity in Pakistan is poorly known. Recent epidemics of dengue fever have revealed the need for more detailed understanding of the diversity and distributions of mosquito species in this region. DNA barcoding improves the accuracy of mosquito inventories because morphological differences between many species are subtle, leading to misidentifications.

METHODOLOGY/PRINCIPAL FINDINGS

Sequence variation in the barcode region of the mitochondrial COI gene was used to identify mosquito species, reveal genetic diversity, and map the distribution of the dengue-vector species in Pakistan. Analysis of 1684 mosquitoes from 491 sites in Punjab and Khyber Pakhtunkhwa during 2010-2013 revealed 32 species with the assemblage dominated by Culex quinquefasciatus (61% of the collection). The genus Aedes (Stegomyia) comprised 15% of the specimens, and was represented by six taxa with the two dengue vector species, Ae. albopictus and Ae. aegypti, dominant and broadly distributed. Anopheles made up another 6% of the catch with An. subpictus dominating. Barcode sequence divergence in conspecific specimens ranged from 0-2.4%, while congeneric species showed from 2.3-17.8% divergence. A global haplotype analysis of disease-vectors showed the presence of multiple haplotypes, although a single haplotype of each dengue-vector species was dominant in most countries. Geographic distribution of Ae. aegypti and Ae. albopictus showed the later species was dominant and found in both rural and urban environments.

CONCLUSIONS

As the first DNA-based analysis of mosquitoes in Pakistan, this study has begun the construction of a barcode reference library for the mosquitoes of this region. Levels of genetic diversity varied among species. Because of its capacity to differentiate species, even those with subtle morphological differences, DNA barcoding aids accurate tracking of vector populations.

Improved growth, drought tolerance, and ultrastructural evidence of increased turgidity in tobacco plants overexpressing Arabidopsis vacuolar pyrophosphatase (AVP1)

An increasing volume of evidence indicating the mechanisms of drought tolerance of AVP1-overexpressing transgenic plants has been reported. In the present study, we are reporting the experiments conducted for the drought tolerance of AVP1 overexpressing plants and WT tobacco plants in three water regimes named as "fully watered," "less-watered," and "desiccated". Results suggest that AVP1 plants exhibited greater vigor and drought tolerance in quantitative terms i.e., increase in size and weight of shoots and capsules. AVP1 plants produced more seeds than WT across all three water regimes. The less-watered regime was found to produce the greatest contrast. AVP1 overexpression enhanced solute accumulation in vacuoles resulting in an increase in water retention and turgor of the cell. The ultrastructure study of AVP1 overexpressing cells and WT leaf cells revealed that AVP1 plants displayed more turgid and hyperosmotic cells than WT. Moreover, guard cells in the AVP1 plants exhibited thick cell walls, few vacuoles, and deep and close stomata, whereas WT plants showed larger vacuoles and relatively open stomata aperture with no significant difference in size and number of the cells per unit area.

Improved growth, drought tolerance, and ultrastructural evidence of increased turgidity in tobacco plants overexpressing Arabidopsis vacuolar pyrophosphatase (AVP1)

An increasing volume of evidence indicating the mechanisms of drought tolerance of AVP1-overexpressing transgenic plants has been reported. In the present study, we are reporting the experiments conducted for the drought tolerance of AVP1 overexpressing plants and WT tobacco plants in three water regimes named as "fully watered," "less-watered," and "desiccated". Results suggest that AVP1 plants exhibited greater vigor and drought tolerance in quantitative terms i.e., increase in size and weight of shoots and capsules. AVP1 plants produced more seeds than WT across all three water regimes. The less-watered regime was found to produce the greatest contrast. AVP1 overexpression enhanced solute accumulation in vacuoles resulting in an increase in water retention and turgor of the cell. The ultrastructure study of AVP1 overexpressing cells and WT leaf cells revealed that AVP1 plants displayed more turgid and hyperosmotic cells than WT. Moreover, guard cells in the AVP1 plants exhibited thick cell walls, few vacuoles, and deep and close stomata, whereas WT plants showed larger vacuoles and relatively open stomata aperture with no significant difference in size and number of the cells per unit area.

Evaluating the capacity of plant DNA barcodes to discriminate species of cotton (Gossypium: Malvaceae)

Although two plastid regions have been adopted as the standard markers for plant DNA barcoding, their limited resolution has provoked the consideration of other gene regions, especially in taxonomically diverse genera. The genus Gossypium (cotton) includes eight diploid genome groups (A-G, and K) and five allotetraploid species which are difficult to discriminate morphologically. In this study, we tested the effectiveness of three widely used markers (matK, rbcL, and ITS2) in the discrimination of 20 diploid and five tetraploid species of cotton. Sequences were analysed locus-wise and in combinations to determine the most effective strategy for species identification. Sequence recovery was high, ranging from 92% to 100% with mean pairwise interspecific distance highest for ITS2 (3.68%) and lowest for rbcL (0.43%). At a 0.5% threshold, the combination of matK+ITS2 produced the greatest number of species clusters. Based on 'best match' analysis, the combination of matK+ITS2 was best, while based on 'all species barcodes' analysis, ITS2 gave the highest percentage of correct species identifications (98.93%). The combination of sequences for all three markers produced the best resolved tree. The disparity index test based on matK+rbcL+ITS2 was significant (P < 0.05) for a higher number of species pairs than the individual gene sequences. Although all three barcodes separated the species with respect to their genome type, no single combination of barcodes could differentiate all the Gossypium species, and tetraploid species were particularly difficult.

Silicon carbide whisker-mediated transformation of cotton (Gossypium hirsutum L.)

Plant transformation methods are invaluable biotechnological tools to generate specific and targeted genetic variation for performance improvement of crop plants. Genetic information is created by proper modification during gene cloning flanked by proper regulatory sequences and delivered to plants via -different plant transformation techniques. Due to being a multipurpose plant, cotton has been subjected to different genetic transformation methods to provide the breeders with an opportunity to develop alien traits or improve the endogenous gene performance that are very difficult or impossible to develop through conventional breeding methods. Here we describe the novel physical way of cotton transformation with different genes by using embryogeneic calli as continuous source of explants.

Development of broad-spectrum insect-resistant tobacco by expression of synthetic cry1Ac and cry2Ab genes

Efficacy of two newly synthesized cry1Ac and cry2Ab genes was checked in tobacco before their expression in cotton. Both genes were artificially synthesized and codon optimized with respect to cotton-preferred codon usage. These genes were cloned in a plant expression vector and then transformed into tobacco. Fifty-eight putative transgenic plants were recovered from the selected explants. Successful integration of both genes in plant genome was confirmed by PCR amplification. Expression of transgenes was confirmed by PCR amplification from total plant RNA. Detached leaf insect bioassays were conducted with Helicoverpa armigera and Spodoptera exigua larvae. About 12 % of the transgenic plants showed significantly high resistance to S. exigua. Significant mortality (62 %) of H. armigera was recorded within 24 h of bioassays. Both toxins showed synergistic effect in tobacco and broadened the spectrum of plant activity against insects.

Engineering broad-spectrum resistance against RNA viruses in potato

RNA silencing technology has become the tool of choice for inducing resistance against viruses in plants. A significant discovery of this technology is that double-stranded RNA (dsRNA), which is diced into small interfering RNAs (siRNAs), is a potent trigger for RNA silencing. By exploiting this phenomenon in transgenic plants, it is possible to confer high level of virus resistance by specific targeting of cognate viral RNA. In order to maximize the efficiency and versatility of the vector-based siRNA approach, we have constructed a chimeric expression vector containing three partial gene sequences derived from the ORF2 gene of Potato virus X, Helper Component Protease gene of Potato virus Y and Coat protein gene of Potato leaf roll virus. Solanum tuberosum cv. Desiree and Kuroda were transformed with this chimeric gene cassette via Agrobacterium tumefaciens-mediated transformation and transgenic status was confirmed by PCR, Southern and double antibody sandwich ELISA detection. Due to simultaneous RNA silencing, as demonstrated by accumulation of specific siRNAs, the expression of partial triple-gene sequence cassette depicted 20% of the transgenic plants are immune against all three viruses. Thus, expression of a single transgene construct can effectively confer resistance to multiple viruses in transgenic plants.

Engineering cotton (Gossypium hirsutum L.) for resistance to cotton leaf curl disease using viral truncated AC1 DNA sequences

Several important biological processes are performed by distinct functional domains found on replication-associated protein (Rep) encoded by AC1 of geminiviruses. Two truncated forms of replicase (tAC1) gene, capable of expressing only the N-terminal 669 bp (5'AC1) and C-terminal 783 bp (3'AC1) nucleotides cloned under transcriptional control of the CaMV35S were introduced into cotton (Gossypium hirsutum L.) using LBA4404 strain of Agrobacterium tumefaciens to make use of an interference strategy for impairing cotton leaf curl virus (CLCuV) infection in transgenic cotton. Compared with nontransformed control, we observed that transgenic cotton plants overexpressing either N-terminal (5'AC1) or C-terminal (3'AC1) sequences confer resistance to CLCuV by inhibiting replication of viral genomic and β satellite DNA components. Molecular analysis by Northern blot hybridization revealed high transgene expression in early and late growth stages associated with inhibition of CLCuV replication. Of the eight T(1) transgenic lines tested, six had delayed and minor symptoms as compared to nontransformed control lines which developed disease symptoms after 2-3 weeks of whitefly-mediated viral delivery. Virus biological assay and growth of T(2) plants proved that transgenic cotton plants overexpressing 5'- and 3'AC1 displayed high resistance level up to 72, 81%, respectively, as compared to non-transformed control plants following inoculation with viruliferous whiteflies giving significantly high cotton seed yield. Progeny analysis of these plants by polymerase chain reaction (PCR), Southern blotting and virus biological assay showed stable transgene, integration, inheritance and cotton leaf curl disease (CLCuD) resistance in two of the eight transgenic lines having single or two transgene insertions. Transgenic cotton expressing partial AC1 gene of CLCuV can be used as virus resistance source in cotton breeding programs aiming to improve virus resistance in cotton crop.

Phase I study of dasatinib in combination with capecitabine, oxaliplatin, and bevacizumab followed by an expanded cohort in previously untreated metastatic colorectal cancer

513

Background: SRC is a non-receptor tyrosine kinase involved in normal and tumor cell signaling functions including cell proliferation, angiogenesis and survival. Dasatinib (D) is a potent inhibitor of SRC kinase activity. Preclinical data suggests the addition of D to standard chemotherapy agents for colon cancer may increase anti-tumor activity. We evaluated D in combination with capecitabine (C), oxaliplatin (O) and bevacizumab (B) in a phase I dose escalation study followed by an expanded cohort in 1st line colorectal.

Methods: For dose escalation, eligible patients had advanced solid tumors with adequate organ and bone marrow function and no increased risk for class-related toxicities. B and O were given intravenously, and C and D were orally administered; cycle length was 21 days. C was dosed at 850 mg/m2 on days 1-14; O was dosed at 130 mg/m2 and B was dosed at 7.5 mg/kg on day one of each cycle. D was dosed at 50 mg twice daily in cohort one and 70 mg once daily in cohort -1. Dose limiting toxicity (DLT) was assessed in cycle 1.

Results: Dose escalation is complete with 10 subjects evaluable for toxicity and 11 subjects evaluable for efficacy. Two DLTs were observed out of 5 evaluable subjects in cohort one. Six evaluable subjects were enrolled in the -1 cohort with 1 DLT. Possible grade ≥ 3 treatment-related adverse events (AEs) included neutropenia, febrile neutropenia, anorexia, diarrhea, fatigue, anemia, hypophosphatemia, hyponatremia and grade 5 GI-perforation. One non-treatment related death was due to disease progression. D-related nausea and fatigue were responsive to low dose oral steroids; fluid retention was responsive to diuretics. Of 10 subjects evaluable for efficacy, 1 subject had a partial response (PR), 2 had a minor response (MR), and 4 had stable disease (SD). Four subjects had disease control (PR, MR, or SD) ≥ 6 months.

Conclusions: D in combination with C, O and B is well-tolerated with a toxicity profile similar to standard C, O and B.The recommended phase II dose is C at 850 mg/m2 on days 1-14, O at 130 mg/m2 and B at 7.5 mg/kg on day one of each cycle, and D at 70 mg once daily. Enrollment in the expanded cohort of 1st line colorectal is ongoing.

[Table: see text]

Pepper leaf curl Lahore virus requires the DNA B component of Tomato leaf curl New Delhi virus to cause leaf curl symptoms

BACKGROUND

Begomoviruses are whitefly-transmitted geminiviruses with genomes that consist of either two components (known as DNA A and DNA B) or a single component (homologous to the DNA A component of bipartite begomoviruses). Monopartite begomoviruses are often associated with a symptom-modulating DNA satellite (collectively known as betasatellites). Both bipartite and monopartite begomoviruses with associated satellites have previously been identified in chillies showing leaf curl symptoms in Pakistan.

RESULTS

A chilli plant (Capsicum annum) with chilli leaf curl disease symptoms was found to contain a begomovirus, a betasatellite and the DNA B component of Tomato leaf curl New Delhi virus (ToLCNDV). The begomovirus consisted of 2747 nucleotides and had the highest sequence identity (99%) with Pepper leaf curl Lahore virus (PepLCLV-[PK: Lah:04], acc. no. AM404179). Agrobacterium-mediated inoculation of the clone to Nicotiana benthamiana, induced very mild symptoms and low levels of viral DNA, detected in systemically infected leaves by PCR. No symptoms were induced in Nicotiana tabacum or chillies either in the presence or absence of a betasatellite. However, inoculation of PepLCLV with the DNA B component of ToLCNDV induced leaf curl symptoms in N. benthamiana, N. tabacum and chillies and viral DNA accumulated to higher levels in comparison to plants infected with just PepLCLV.

CONCLUSIONS

Based on our previous efforts aimed at understanding of diversity of begomoviruses associated with chillies, we propose that PepLCLV was recently mobilized into chillies upon its interaction with DNA B of ToLCNDV. Interestingly, the putative rep-binding iterons found on PepLCLV (GGGGAC) differ at two base positions from those of ToLCNDV (GGTGTC). This is the first experimental demonstration of the infectivity for a bipartite begomovirus causing chilli leaf curl disease in chillies from Pakistan and suggests that component capture is contributing to the emerging complexity of begomovirus diseases in the region.

Codon optimization of cry1Ab gene for hyper expression in plant organelles

With the advent of genetic manipulation techniques, it has become possible to clone and insert gene into the genome of crop plants to confer resistance to insects and pests. Resistance to insects has been demonstrating in transgenic plants either by triggering defense system of plants or by expressing heterologous cry genes for delta-endotoxins from Bacillus thuringiensis. In the present study, synthetic cry1Ab gene was developed with optimized chloroplast preferred codons and is expressed in tobacco plastid genome called plastome, following chloroplast transformation strategy, which is environment friendly technique to minimize out-crossing of transgenes to related weeds and crops. In addition, due to high polyploidy of plastid genome transformation of chloroplast permits the introduction of thousands of copies of foreign genes per plant cell, leading to extraordinarily high levels of foreign protein expression. The chloroplast transformation technology aims to insert stably into the plastome through homologous recombination into pre-decided position. To characterize the synthetic cry1Ab gene, chloroplast transformation vectors were developed and bombarded to the leaf cells of tobacco plants maintained under aseptic conditions. After bombardment, the drug resistant shoots were selected and regenerated on drug containing regeneration medium. Homoplasmic shoots were recovered after successive rounds of selection and regeneration. Proliferated plants were subjected to genomic DNA analysis by using polymerase chain reaction (PCR) technique where cry1Ab gene-specific primers were used. PCR positive plants were subjected to protein analysis, and functionally expressed proteins were detected using Immuno-Strips specific for cry1Ab/Ac gene products. Transgenic plants carrying cry1Ab gene were found expressing Bt toxins confirming that engineered gene could be expressed in other plants as well.

Factors associated with chemotherapy receipt and intensity for stage IV colorectal cancer (CRC): A multihealth system, population-based study

6519

Background: Little is known about chemotherapy practice patterns for patients with stage IV CRC. Methods: Cancer Outcomes Research & Surveillance Consortium (CanCORS) is a prospective cohort study including patients with incident CRC sampled from a set of defined populations and health systems. Eligible patients for this analysis (n = 742) had stage IV CRC and abstracted medical record data, including stage, chemotherapy, comorbidity (measured by the Adult Comorbidity Evaluation 27 index), and sociodemographic data. Logistic regression models were used to evaluate factors associated with chemotherapy receipt and intensity. Results: A majority of patients were male (62%) and white (62%). 27% were ≥75 years old, and 14% had severe comorbidity. 34% had private insurance, 32% had public insurance (including Medicare/Medicaid), 18% were Veterans Affairs patients, 4% had no insurance, and 13% were missing insurance information. Overall, 77% received chemotherapy, and 57% received >1 line of therapy. Patients were less likely to receive chemotherapy if they were older (65–74 vs. <55 years = adjusted odds ratio [OR] 0.14, 95%CI 0.06–0.33, p < 0.001; ≥75 vs. <55 years = OR 0.04, 95%CI 0.02–0.64, p < 0.001), or had severe comorbidity (OR 0.38; 95%CI 0.23–0.64; p < 0.001). When treated, patients ≥75 years were more likely to receive capecitabine vs. 5-fluorouracil (5-FU) (p < 0.001), less likely to receive >1 line of therapy (p < 0.001), and less likely to receive oxaliplatin or irinotecan combination therapy vs. a single-agent fluorouracil (p < 0.001). Although only 4% were uninsured, lack of insurance did not appear to be a factor in receipt of chemotherapy. Patients with public vs. private insurance were more likely to receive chemotherapy (OR 2.58; 95%CI 1.49–4.47; p < 0.001) but were less likely to receive combination therapy versus a single-agent 5-FU (p = 0.02). Conclusions: The elderly are less likely to receive standard therapy. While patients with public insurance are more likely to receive chemotherapy, they are less likely to receive recommended first-line combination regimens. Future research should investigate how insurance coverage and demographics influence physician and patient preferences for advanced CRC treatment.

No significant financial relationships to disclose.

Silicon carbide whisker-mediated embryogenic callus transformation of cotton (Gossypium hirsutum L.) and regeneration of salt tolerant plants

A silicon carbide whisker-mediated gene transfer system with recovery of fertile and stable transformants was developed for cotton (Gossypium hirsutum L.) cv. Coker-312. Two-month-old hypocotyl-derived embryogenic/non-embryogenic calli at different days after subculture were treated with silicon carbide whiskers for 2 min in order to deliver pGreen0029 encoding GUS gene and pRG229 AVP1 gene, encoding Arabidopsis vacuolar pyrophosphatase, having neomycin phosphotransferaseII (nptII) genes as plant-selectable markers. Three crucial transformation parameters, i.e., callus type, days after subculture and selection marker concentration for transformation of cotton calli were evaluated for optimum efficiency of cotton embryogenic callus transformation giving upto 94% transformation efficiency. Within six weeks, emergence of kanamycin-resistant (kmr) callus colonies was noted on selection medium. GUS and Southern blot analysis showed expression of intact and multiple transgene copies in the transformed tissues. Kanamycin wiping of leaves from T1, T2, and T3 progeny plants revealed that transgenes were inherited in a Mendelian fashion. Salt treatment of T1 AVP1 transgenic cotton plants showed significant enhancement in salt tolerance as compared to control plants. Thus far, this is first viable physical procedure after particle bombardment available for cotton that successfully can be used to generate fertile cotton transformants.

The hypersensitive response to tomato leaf curl New Delhi virus nuclear shuttle protein is inhibited by transcriptional activator protein

The hypersensitive response (HR) is a common feature of plant disease resistance reactions and a type of programmed cell death (PCD). Many pathogens are able to modulate pathways involved in cell death. In contrast to animal viruses, inhibitors of PCD activity have not been identified for plant-infecting viruses. Previously, we have reported that the nuclear shuttle protein (NSP) of Tomato leaf curl New Delhi virus (ToLCNDV) induces an HR in Nicotiana tabacum and Lycopersicon esculentum plants when expressed under the control of the Cauliflower mosaic virus 35S promoter. However, HR is not evident in plants infected with ToLCNDV, suggesting that the virus encodes a factor (or factors) that counters this response. Analysis of all ToLCNDV-encoded genes pinpointed the transcriptional activator protein (TrAP) as the factor mediating the anti-HR effect. Deletion mutagenesis showed the central region of TrAP, containing a zinc finger domain and nuclear localization signal, to be important in inhibiting the HR. These results demonstrate that TrAP counters HR-induced cell death, the first such activity identified for a plant-infecting virus.

A monopartite begomovirus-associated DNA beta satellite substitutes for the DNA B of a bipartite begomovirus to permit systemic infection

DNA beta is a circular single-stranded satellite DNA which co-infects with certain monopartite helper begomoviruses to cause economically important diseases, such as cotton leaf curl disease (CLCuD). DNA beta encodes a single protein, betaC1. Tomato leaf curl New Delhi virus (ToLCNDV) is a bipartite begomovirus in which both DNA A and DNA B are required for systemic infection. Inoculation of tomato plants with ToLCNDV DNA A alone induced local but not systemic infection, whereas co-inoculation with DNA A and the DNA beta associated with CLCuD resulted in systemic infection. DNA beta containing a disrupted betaC1 open reading frame (ORF) did not mobilize DNA A systemically. Co-inoculation of plants with DNA A and a construct of the betaC1 ORF, under the control of the cauliflower mosaic virus 35S promoter, resulted in the systemic movement of DNA A. In inoculated tobacco and onion epidermal cells, betaC1 fused to GFP was localized at the cell periphery in association with punctate bodies, around and within the cell nucleus and with the endoplasmic reticulum. It is concluded that heterologous betaC1 protein can replace the movement function of the DNA B of a bipartite begomovirus. Evidence is also provided that tomato leaf curl virus-encoded C4 protein confers the same movement function to ToLCNDV DNA A. The intracellular distribution of betaC1 is consistent with the hypothesis that it has a role in transporting the DNA A from the nuclear site of replication to the plasmodesmatal exit sites of the infected cell.

Development of agriculture biotechnology in Pakistan

Agriculture plays an important role in the national economy of Pakistan, where most of the rapidly increasing population resides in rural areas and depends on agriculture for subsistence. Biotechnology has considerable potential for promoting the efficiency of crop improvement, food production, and poverty reduction. Use of modern biotechnology started in Pakistan since 1985. Currently, there are 29 biotech centers/institutes in the country. However, few centers have appropriate physical facilities and trained manpower to develop genetically modified (GM) crops. Most of the activities have been on rice and cotton, which are among the top 5 crops of Pakistan. Biotic (virus/bacterial/insect) and abiotic (salt) resistant and quality (male sterility) genes have already been incorporated in some crop plants. Despite acquiring capacity to produce transgenic plants, no GM crops, either produced locally or imported, have been released in the country. Pakistan is signatory to the World Trade Organization, Convention on Biological Diversity, and Cartagena protocols. Several legislations under the Agreement on Trade-Related Aspects of Intellectual Property Rights have been promulgated in the country. National Biosafety Guidelines have been promulgated in April 2005. The Plant Breeders Rights Act, Amendment in Seed Act-1976, and Geographical Indication for Goods are still passing through discussion, evaluation, and analysis phases. Meanwhile, an illegal GM crop (cotton) has already sneaked into farmer's field. Concerted and coordinated efforts are needed among various ministries for implementation of regulation and capacity building for import/export and local handling of GM crops. Pakistan could easily benefit from the experience of Asian countries, especially China and India, where conditions are similar and the agriculture sector is almost like that of Pakistan. Thus, the exchange of information and experiences is important among these nations.

Comorbidity, age and stage at diagnosis in colorectal cancer (CRC)

6554

Background: Stage at diagnosis is a crucial predictor of outcome in CRC. The purpose of this study is to determine if comorbidity and age affect the stage at which CRC is diagnosed. Identifying variables that influence stage might improve outcomes in CRC. Due to frequent contact with the health care system, we hypothesize that patients with greater comorbidity and older age are more likely to be diagnosed with early-stage disease. Methods: We present data from two distinct patient populations: using the Cancer Care Outcomes Research and Surveillance Consortium (CanCORS) database, we identified CRC patients treated at 15 Veterans Administration (VA) hospitals from 2003-present. We also identified CRC patients treated from 2003-present at 10 non-VA, fee-for-service (FFS) practices in North and South Carolina. Data were abstracted by retrospective chart review. Comorbidity was calculated by the Charlson comorbidity index (CCI) with high comorbidity defined as CCI =3. Older age was defined as age =70 years. Data were analyzed using logistic regression where the odds of late stage at diagnosis were modeled as influenced by older age, high CCI, and race. The analysis included estimation of adjusted and unadjusted odds ratios. Results: 347 VA and 282 FFS patients were included. 98% VA vs 50% FFS were male; 43% VA vs 27% FFS were aged =70; 56% VA vs 70% FFS were white; 26% VA vs 44% FFS presented with metastatic CRC; and 21% VA vs 6% FFS had a CCI =3. In both patient populations, regression analysis showed that older age, high CCI and white race were not significant predictors of stage at diagnosis. VA 95% confidence intervals (CI's) were 0.52–1.41 (age =70), 0.50–1.75 (CCI =3), and 0.42–1.11 (white race). FFS 95% CI's were 0.52–1.53 (age =70), 0.36–2.78 (CCI =3), and 0.74–2.11 (white race). Broader 95% CI's in the FFS analysis were due to smaller sample size. Conclusions: In CRC patients, age and comorbidity were not related to stage at diagnosis. The findings are similar whether the patients were treated in a fee-for-service or VA health system. While older age and greater illness might provide more contact with the health care system, this exposure did not result in earlier diagnosis of CRC. Future studies will examine the impact of comorbidity on CRC treatment and survival.

No significant financial relationships to disclose.

Choice of adjuvant and first-line metastatic chemotherapy (CT) for colorectal cancer (CRC) treated in the Carolinas

17039

Background: CT choice is influenced by many factors including published evidence, guidelines, cost, reimbursement, patient considerations, key opinion leaders, and anecdote. Substantial locoregional variation in practice patterns can exist, and therefore studies of locoregional practice provide important information on local drivers of care. Methods: Using a population-based strategy, we identified CRC patients who developed metastatic disease since 6/1/03 from 9 Duke Oncology Network community practices and 1 academic practice in North and South Carolina. Demographic, comorbidity, diagnostic, stage, initial treatment, and metastatic treatment data were abstracted by retrospective chart review, double-entered and verified for accuracy. Results: Of the first 743 charts screened, 306 were eligible (mean age 61 (SD 13), 49% male; 65% white; 22% black; 77% colon cancer and 19% rectal; stages II 8%, III 16%, IV 64%). 26 earlier stage rectal cancer patients received neoadjuvant treatment, 50% infusional fluorouracil (5FU) and 42% capecitabine (Cap). 46 colon cancer patients received adjuvant CT, including 5FU/leucovorin (LVN; 54%), 5FU/LVN/oxaliplatin (21%), Cap (9%), and 5FU/LVN/irinotecan (7%). First-line CT for metastatic colon cancer (n=149) included FOLFOX+-bevacizumab (Bev; 42%), Cap/oxaliplatin +- Bev (23%), 5FU/LVN + Bev (9%), FOLFIRI +- Bev (7%), IFL +- Bev (7%), clinical trial (7%), Cap (3%), and unknown (1%). 54% of patients received Bev overall, reflecting 49% usage before 6/05 and 69% after 6/05. CT was not offered for 25 (8%) at initial diagnosis. Conclusion: Locoregional practice patterns in the Carolinas suggest that for adjuvant treatment of CRC, oxaliplatin has been used in 21% of adjuvant and 75% of first-line metastatic colon CT regimens, and that bevacizumab use has increased to 69% of first-line metastatic CRC patients.

No significant financial relationships to disclose.

RNAi-mediated male sterility of tobacco by silencing TA29

The superior performance of F1 hybrids has a significant impact on agricultural productivity. For commercial application, the availability of an efficient system for obtaining male-sterile lines of crops is an essential prerequisite. Here we have investigated the use of RNA interference (RNAi) technology to silence a male-specific gene in the model host tobacco. TA29 is expressed exclusively in anthers at the time of microspore development. About 10 out of 13 tobacco lines transformed with a hairpin RNAi construct containing TA29 sequences were male sterile. Transgenic plants were phenotypically indistinguishable from non-transgenic plants. At the anthesis stage, pollen grains from transgenic, male-sterile plants were aborted and lysed in comparison to the round and fully developed pollen in non-transgenic plants. Microscopic analysis of anthers showed selective degradation of tapetum in transgenic plants with no microspore development. One week after self-pollination, the ovules of non-transgenic plants were double the size of those in transgenic plants, due to successful self-fertilization. Male sterile transgenic plants set seed normally, when cross-pollinated with pollen from non-transgenic plants, confirming no adverse effect on the female parts of the flower. These results show that silencing of male-specific genes by RNAi is potentially a useful tool for generating male-sterile lines for producing hybrid seed.

Silencing of the AV2 gene by antisense RNA protects transgenic plants against a bipartite begomovirus

Whitefly-transmitted geminiviruses (genus Begomovirus) are phytopathogens that cause heavy losses to crops worldwide. Efforts to engineer resistance against these viruses are focused mainly on silencing of complementary-sense virus genes involved in virus replication. Here we have targeted a virion-sense gene (AV2) to develop resistance against Tomato leaf curl New Delhi virus, a bipartite begomovirus prevalent throughout the Indian subcontinent. We show that tobacco plants transformed with an antisense construct targeting this gene are resistant to the virus. Following challenged with the virus, transgenic plants remained symptomless, although viral DNA could be detected in some plants by PCR. This is the first report of transgenic resistance against a bipartite begomovirus obtained by targeting a virion-sense gene. The relatively conserved nature of the gene suggests that the technology may be useful to develop broad-spectrum resistance which is required because of the fact that plants are often infected with multiple begomoviruses in the field.

Engineering novel traits in plants through RNA interference

RNA interference (RNAi) is a homology-dependent gene silencing technology that involves double-stranded RNA directed against a target gene or its promoter region. Using hairpin constructs, double-stranded RNA can be expressed in plants relatively easily, enabling this technology to be applied to a wide range of species to silence the expression of both specific endogenous genes and genes of invading pathogens. RNAi has also been used to engineer metabolic pathways to overproduce secondary products with health, yield or environmental benefits. The application of tissue-specific or inducible gene silencing, with the use of appropriate promoters, and the ability to silence several genes simultaneously should enhance our ability to create novel traits in plants.

Preliminary results of a phase I study of bevacizumab (BV) in combination with everolimus (E) in patients with advanced solid tumors

3097

Background: BV is a potent inhibitor of vascular endothelial growth factor (VEGF) with broad clinical activity. E is an mTOR (mammalian target of rapamycin) inhibitor in development for cancer and solid organ transplant therapy. VEGF and mTOR inhibitors have anti-tumor and anti-angiogenesis effects alone and in combination in preclinical models. As a combination anti-angiogenesis therapy, we evaluated BV + E in a phase I, pharmacokinetic (PK), biomarker study. Methods: BV was dosed at 10mg/kg IV q14d. E was dosed at 5mg PO QD, escalating to 10mg QD. Cycle length was 28 days. DLT was defined as any grade 4 heme or grade 3/4 non-heme event in Cycle 1 related to treatment. Pts had advanced solid tumors, adequate organ function, and no increased risks for class-related toxicities. Serial blood samples were collected for PK studies of E. Dermal wound angiogenesis assays were performed pre and on treatment for phospho VEGFR2, AKT, mTOR, and S6K. Results: 14 pts have been enrolled (8 F, 6 M), 12 evaluable for toxicity, 14 for efficacy. Median age is 58y (range 29–73). At dose level 1 (BV 10mg/E 5mg) there were no DLT’s in 5 pts. At dose level 2 (BV 10mg/E 10mg), no DLT’s were noted in the initial 3 pts and the cohort was expanded to 9 pts. Side effects were primarily grade 1–2: pain (10/14), mucositis (9/14), anorexia (8/14), rash (7/14), bleeding (7/14), hyperlipidemia (6/14), fatigue (6/14), and HTN (4/14). 1 pt had a myocardial infarction at day 72 and one pt developed nephrotic syndrome at day 70. 7/14 pts had stable disease as best response (70–278d). Conclusions: BV + E is generally well-tolerated. Preliminary clinical activity and class-related side effects were noted. The recommended phase II dose is BV 10mg/kg IV q14d and E 10mg PO QD.

[Table: see text]

First Report of Cotton Leaf Curl Disease in Central and Southern Sindh Province in Pakistan

Cotton leaf curl is a devastating disease of cotton that has resulted in severe losses (estimated at more than US$87 million per annum) in Pakistan. The epidemic is centered in Punjab, the province that contributes approximately 80% of Pakistan's cotton. Previously, the disease had been observed sporadically on single plants in the northern Sindh Province but did not cause economically significant damage. During the years 2004 and 2005, a high incidence (approximately 20%) of the disease was observed in Shahdadpur and parts of District Sanghar, located in central Sindh Province. The disease was also observed at low incidence (<1%) in southern Sindh. To confirm the identity of the causal agent of the disease, 18 samples from three districts in central southern Sindh (Sanghar, Hala, and Hyderabad) were collected, and total DNA was extracted using cetyltrimethylammoniumbromide (2). Universal primers for begomoviruses based on conserved sequences as follows were used in polymerase chain reaction (PCR): BegomoF (5'-CCGTGCTGCTGCCCCCATTGTCCGCGTCAC-3') and BegomoR (5'-CTGCCACAACCATGGATTCACGCACAGGG-3'). Universal primers for amplification of DNA β with PCR were also used (1). A full-length clone of Cotton leaf curl Multan virus (CLCuMV) was labeled with alpha-³²PdCTP by the oligo-labeling method and used as a probe in Southern hybridization for the detection of geminivirus DNA forms (2). Similarly, cotton leaf curl disease associated DNA β was also labeled and used as a probe in Southern hybridization. The use of universal primers for begomoviruses resulted in amplification of viral DNA of the expected size from all samples while no PCR product was obtained from healthy plants. PCR results confirmed that all plants were infected with begomoviruses. Southern hybridization with CLCuMV and DNA β probes detected begomovirus DNA forms associated with virus replication when washed at medium stringency, further confirming that the plants were infected with the cotton leaf curl geminivirus complex (2). Our results indicate that cotton leaf curl complex has become established in central and southern districts of Sindh Province and it poses a major threat to cotton grown in the region. References: (1) R. W. Briddon et al. Mol. Biotechnol. 20:315, 2002. (2). S. Mansoor et al. Arch. Virol. 148:1969, 2003.

Spider venom toxin protects plants from insect attack

Many of the toxin proteins, that have been heterogeneously expressed in agricultural crops to provide resistance to insect pests, are too specific or are only mildly effective against the major insect pests. Spider venoms are a complex cocktail of toxins that have evolved specifically to kill insects. Here we show that the omega-ACTX-Hv1a toxin (Hvt), a component of the venom of the Australian funnel web spider (Hadronyche versuta) that is a calcium channel antagonist, retains its biological activity when expressed in a heterologous system. Expressed as a fusion protein in E. coli, the purified toxin fusion immobilized and killed Helicoverpa armigera and Spodoptera littoralis caterpillars when applied topically. Transgenic expression of Hvt in tobacco effectively protected the plants from H. armigera and S. littoralis larvae, with 100% mortality within 48 h. We conclude that the Hvt is an attractive and effective molecule for the transgenic protection of plants from herbivorous insects which should be evaluated further for possible application in agriculture.