Gene doctoring: a method for recombineering in laboratory and pathogenic Escherichia coli strains

Background  

Homologous recombination mediated by the λ-Red genes is a common method for making chromosomal modifications in Escherichia coli. Several protocols have been developed that differ in the mechanisms by which DNA, carrying regions homologous to the chromosome, are delivered into the cell. A common technique is to electroporate linear DNA fragments into cells. Alternatively, DNA fragments are generated in vivo by digestion of a donor plasmid with a nuclease that does not cleave the host genome. In both cases the λ-Red gene products recombine homologous regions carried on the linear DNA fragments with the chromosome. We have successfully used both techniques to generate chromosomal mutations in E. coli K-12 strains. However, we have had limited success with these λ-Red based recombination techniques in pathogenic E. coli strains, which has led us to develop an enhanced protocol for recombineering in such strains.     

Genotypic differences in thermotolerance are dependent upon prestress capacity for antioxidant protection of the photosynthetic apparatus in Gossypium hirsutum

Numerous studies have illustrated the need for antioxidant enzymes in acquired photosynthetic thermotolerance, but information on their possible role in promoting innate thermotolerance is lacking. We investigated the hypothesis that genotypic differences in source leaf photosynthetic thermostability would be dependent upon prestress capacity for antioxidant protection of the photosynthetic apparatus in Gossypium hirsutum. To test this hypothesis, thermosensitive (cv. ST4554) and reportedly thermotolerant (cv. VH260) G. hirsutum plants were exposed to control (30/20°C) or high‐day temperature (38/20°C) conditions during flowering and source leaf gas exchange, chlorophyll content and maximum photochemical efficiency (F_v/F_m) were measured for each treatment. The relationship between source leaf thermostability and prestress antioxidant capacity was quantified by monitoring the actual quantum yield response of photosystem II (PSII) (Φ_PSII) to a range of temperatures for both cultivars grown under the control temperature regime and measuring antioxidant enzyme activity for those same leaves. VH260 was more thermotolerant than ST4554 as evidenced by photosynthesis and F_v/F_m being significantly lower under high temperature for ST4554 but not VH260. Under identical growth conditions, VH260 had significantly higher optimal and threshold temperatures for Φ_PSII and glutathione reductase (GR; EC 1.8.1.7) activity than ST4554, and innate threshold temperature was dependent upon endogenous GR and superoxide dismutase (SOD; EC 1.15.1.1) activity. We conclude that maintaining a sufficient antioxidant enzyme pool prior to heat stress is an innate mechanism for coping with rapid leaf temperature increases that commonly occur under field conditions.     

Novel IL10 gene family associations with systemic juvenile idiopathic arthritis

Juvenile idiopathic arthritis (JIA) is the most common cause of chronic childhood disability and encompasses a number of disease subgroups. In this study we have focused on systemic JIA (sJIA), which accounts for approximately 11% of UK JIA cases. This study reports the investigation of three members of the IL10 gene family as candidate susceptibility loci in children with sJIA. DNA from 473 unaffected controls and 172 patients with sJIA was genotyped for a single nucleotide polymorphism (SNP) in IL19 and IL20 and two SNPs in IL10. We examined evidence for association of the four SNPs by single marker and haplotype analysis. Significant differences in allele frequency were observed between cases and controls, for both IL10-1082 (p = 0.031) and IL20-468 (p = 0.028). Furthermore, examination of the haplotypes of IL10-1082 and IL20-468 revealed greater evidence for association (global p = 0.0006). This study demonstrates a significant increased prevalence of the low expressing IL10-1082 genotype in patients with sJIA. In addition, we show a separate association with an IL20 polymorphism, and the IL10-1082A/IL20-468T haplotype. The two marker 'A-T' haplotype confers an odds ratio of 2.24 for sJIA. This positive association suggests an important role for these cytokines in sJIA pathogenesis.     

High-throughput screen identifies disulfiram as a potential therapeutic for triple-negative breast cancer cells: Interaction with IQ motif-containing factors

Triple-negative breast cancer (TNBC) represents an aggressive subtype, for which radiation and chemotherapy are the only options. Here we describe the identification of disulfiram, an FDA-approved drug used to treat alcoholism, as well as the related compound thiram, as the most potent growth inhibitors following high-throughput screens of 3185 compounds against multiple TNBC cell lines. The average IC₅₀ for disulfiram was ~300 nM. Drug affinity responsive target stability (DARTS) analysis identified IQ motif-containing factors IQGAP1 and MYH9 as direct binding targets of disulfiram. Indeed, knockdown of these factors reduced, though did not completely abolish, cell growth. Combination treatment with 4 different drugs commonly used to treat TNBC revealed that disulfiram synergizes most effectively with doxorubicin to inhibit cell growth of TNBC cells. Disulfiram and doxorubicin cooperated to induce cell death as well as cellular senescence, and targeted the ESA⁺/CD24^-/low/CD44⁺ cancer stem cell population. Our results suggest that disulfiram may be repurposed to treat TNBC in combination with doxorubicin.     

Differential Sensitivities of Fast- and Slow-Cycling Cancer Cells to Inosine Monophosphate Dehydrogenase 2 Inhibition by Mycophenolic Acid

As uncontrolled cell proliferation requires nucleotide biosynthesis, inhibiting enzymes that mediate nucleotide biosynthesis constitutes a rational approach to the management of oncological diseases. In practice, however, results of this strategy are mixed and thus elucidation of the mechanisms by which cancer cells evade the effect of nucleotide biosynthesis restriction is urgently needed. Here we explored the notion that intrinsic differences in cancer cell cycle velocity are important in the resistance toward inhibition of inosine monophosphate dehydrogenase (IMPDH) by mycophenolic acid (MPA). In short-term experiments, MPA treatment of fast-growing cancer cells effectively elicited G0/G1 arrest and provoked apoptosis, thus inhibiting cell proliferation and colony formation. Forced expression of a mutated IMPDH2, lacking a binding site for MPA but retaining enzymatic activity, resulted in complete resistance of cancer cells to MPA. In nude mice subcutaneously engrafted with HeLa cells, MPA moderately delayed tumor formation by inhibiting cell proliferation and inducing apoptosis. Importantly, we developed a lentiviral vector–based Tet-on label-retaining system that enables to identify, isolate and functionally characterize slow-cycling or so-called label-retaining cells (LRCs) in vitro and in vivo. We surprisingly found the presence of LRCs in fast-growing tumors. LRCs were superior in colony formation, tumor initiation and resistance to MPA as compared with fast-cycling cells. Thus, the slow-cycling compartment of cancer seems predominantly responsible for resistance to MPA.     

A 46,XY female DSD patient with bilateral gonadoblastoma, a novel SRY missense mutation combined with a WT1 KTS splice-site mutation

Patients with Disorders of Sex Development (DSD), especially those with gonadal dysgenesis and hypovirilization are at risk of developing malignant type II germ cell tumors/cancer (GCC) (seminoma/dysgerminoma and nonseminoma), with either carcinoma in situ (CIS) or gonadoblastoma (GB) as precursor lesion. In 10-15% of 46,XY gonadal dysgenesis cases (i.e., Swyer syndrome), SRY mutations, residing in the HMG (High Mobility Group) domain, are found to affect nuclear transport or binding to and bending of DNA. Frasier syndrome (FS) is characterized by gonadal dysgenesis with a high risk for development of GB as well as chronic renal failure in early adulthood, and is known to arise from a splice site mutation in intron 9 of the Wilms' tumor 1 gene (WT1). Mutations in SRY as well as WT1 can lead to diminished expression and function of SRY, resulting in sub-optimal SOX9 expression, Sertoli cell formation and subsequent lack of proper testicular development. Embryonic germ cells residing in this unfavourable micro-environment have an increased risk for malignant transformation. Here a unique case of a phenotypically normal female (age 22 years) is reported, presenting with primary amenorrhoea, later diagnosed as hypergonadotropic hypogonadism on the basis of 46,XY gonadal dygenesis with a novel missense mutation in SRY. Functional in vitro studies showed no convincing protein malfunctioning. Laparoscopic examination revealed streak ovaries and a normal, but small, uterus. Pathological examination demonstrated bilateral GB and dysgerminoma, confirmed by immunohistochemistry. Occurrence of a delayed progressive kidney failure (focal segmental glomerular sclerosis) triggered analysis of WT1, revealing a pathogenic splice-site mutation in intron 9. Analysis of the SRY gene in an additional five FS cases did not reveal any mutations. The case presented shows the importance of multi-gene based diagnosis of DSD patients, allowing early diagnosis and treatment, thus preventing putative development of an invasive cancer.     

Immune response of mice exposed to cis-diamminedichloroplatinum

Summary The effects of cis-diamminedichloroplatinum (CDDP) on lymphoid organs and the immune response of young and older adult mice were studied histologically and by functionally assessing the activity of various subpopulations of immune cells. Young adult mice (6–8 weeks old) treated with 2 mg/kg CDDP mounted an enhanced splenic plaque-forming cell (PFC) response to both sheep erythrocytes, a helper T-cell-dependent antigen (HD), and pneumococcal polysaccharide type III a helper T-cell-independent antigen (HI). Older adult mice (18–22 weeks old) treated in the same way exhibited an equally enhanced PFC response to HD antigen and even a more pronounced response to HI antigen. Treatment of mice with 12 mg/kg CDDP resulted in immunosuppression. Thymus, lymph nodes, and spleen of animals treated with the higher dose of CDDP showed a marked cell depletion from both T and B areas, confirming that the immunosuppression was due to an indiscriminate elimination of both T and B lymphocytes. The immunosuppression and the cell depletion from lymphoid organs were more pronounced in younger mice. Thus, the effects of CDDP on the lymphoid organs and the immune response depend both on the age of the animals and on the dose of the drug. CDDP given in small doses enhances the PFC response, whereas a reduced PFC response is obtained following high-dose treatment. Abbreviations used: CDDP, cis-diamminedichloroplatinum; PFC, plaque-forming cell; HD, helper T-cell dependent; HI, helper T cell-independent; SIII, pneumococcal polysaccharide type III; SRBC, sheep red blood cells; TNP, trinitrophenyl; KLH, keyhole limpet hemocyanin; TNBS, 2, 4, 6-trinitrobenzene sulfonic acid; BBS, borate-buffered saline     

Decline in photosynthesis as related to alterations in chloroplast ultrastructure of a cotton leaf during ontogeny

Field studies were conducted to investigate ontogenic changes in leaf photosynthesis and chloroplast ultrastructure of a single cotton (Gossypium hirsutum L.) leaf subtending the fruit. A 20-d old leaf was the most physiologically active with net photosynthetic rate (PN) of 16.5 mol m-2 s-1 and nitrogen (N) concentration of 168 mmol m-2. These values declined with leaf age and a close relationship existed between them. Concurrent with declines in PN, ultrastructural alterations occurred in the chloroplast: the 20-d old leaf had increased grana number and thylakoids per granum and a few plastoglobuli. Afterwards, the grana number and thylakoids per granum declined with leaf age indicating disintegrated grana and stroma lamellae. Concomitant with disintegrated membrane system was the presence of numerous large plastoglobuli. The PN was closely related to grana number and thylakoids per granum suggesting that the decline in PN with leaf age was associated with ultrastructural changes in the chloroplast.     

Water use efficiency as a function of leaf age and position within the cotton canopy

The gas exchange properties of whole plant canopies are an integral part of crop productivity and have attracted much attention in recent years. However, insufficient information exists on the coordination of transpiration and CO₂ uptake for individual leaves during the growing season. Single-leaf determinations of net photosynthesis (Pn), transpiration (E) and water use efficiency (WUE) for field-grown cotton (Gossypium hirsutum L.) leaves were recorded during a 2-year field study. Measurements were made at 3 to 4 day intervals on the main-stem and first three sympodial leaves at main-stem node 10 from their unfolding through senescence. Results indicated that all gas exchange parameters changed with individual main-stem and sympodial leaf age. Values of Pn, E and WUE followed a rise and fall pattern with maximum rates achieved at a leaf age of 18 to 20 days. While no significant position effects were observed for Pn, main-stem and sympodial leaves did differ in E and WUE particularly as leaves aged beyond 40 days. For a given leaf age, the main-stem leaf had a significantly lower WUE than the three sympodial leaves. WUE's for the main-stem and three sympodial leaves between the ages of 41 to 50 days were 0.85, 1.30, 1.36 and 1.95 μmol CO₂ mmol⁻¹ H₂O, respectively. The mechanisms which mediated leaf positional differences for WUE were not strictly related to changes in stomatal conductance (g_s·H₂O) since decreases in g_s·H₂O with leaf age were similar for the four leaves. However, significantly different radiant environments with distance along the fruiting branch did indicate the possible involvement of mutual leaf shading in determining WUE. The significance of these findings are presented in relation to light competition within the plant canopy during development.