Commercial Crop Yields Reveal Strengths and Weaknesses for Organic Agriculture in the United States

Land area devoted to organic agriculture has increased steadily over the last 20 years in the United States, and elsewhere around the world. A primary criticism of organic agriculture is lower yield compared to non-organic systems. Previous analyses documenting the yield deficiency in organic production have relied mostly on data generated under experimental conditions, but these studies do not necessarily reflect the full range of innovation or practical limitations that are part of commercial agriculture. The analysis we present here offers a new perspective, based on organic yield data collected from over 10,000 organic farmers representing nearly 800,000 hectares of organic farmland. We used publicly available data from the United States Department of Agriculture to estimate yield differences between organic and conventional production methods for the 2014 production year. Similar to previous work, organic crop yields in our analysis were lower than conventional crop yields for most crops. Averaged across all crops, organic yield averaged 80% of conventional yield. However, several crops had no significant difference in yields between organic and conventional production, and organic yields surpassed conventional yields for some hay crops. The organic to conventional yield ratio varied widely among crops, and in some cases, among locations within a crop. For soybean (Glycine max) and potato (Solanum tuberosum), organic yield was more similar to conventional yield in states where conventional yield was greatest. The opposite trend was observed for barley (Hordeum vulgare), wheat (Triticum aestevum), and hay crops, however, suggesting the geographical yield potential has an inconsistent effect on the organic yield gap.     

Multiplex PCR and Next Generation Sequencing for the Non-Invasive Detection of Bladder Cancer

Background

Highly sensitive and specific urine-based tests to detect either primary or recurrent bladder cancer have proved elusive to date. Our ever increasing knowledge of the genomic aberrations in bladder cancer should enable the development of such tests based on urinary DNA.

Methods

DNA was extracted from urine cell pellets and PCR used to amplify the regions of the TERT promoter and coding regions of FGFR3, PIK3CA, TP53, HRAS, KDM6A and RXRA which are frequently mutated in bladder cancer. The PCR products were barcoded, pooled and paired-end 2 x 250 bp sequencing performed on an Illumina MiSeq. Urinary DNA was analysed from 20 non-cancer controls, 120 primary bladder cancer patients (41 pTa, 40 pT1, 39 pT2+) and 91 bladder cancer patients post-TURBT (89 cancer-free).

Results

Despite the small quantities of DNA extracted from some urine cell pellets, 96% of the samples yielded mean read depths >500. Analysing only previously reported point mutations, TERT mutations were found in 55% of patients with bladder cancer (independent of stage), FGFR3 mutations in 30% of patients with bladder cancer, PIK3CA in 14% and TP53 mutations in 12% of patients with bladder cancer. Overall, these previously reported bladder cancer mutations were detected in 86 out of 122 bladder cancer patients (70% sensitivity) and in only 3 out of 109 patients with no detectable bladder cancer (97% specificity).

Conclusion

This simple, cost-effective approach could be used for the non-invasive surveillance of patients with non-muscle-invasive bladder cancers harbouring these mutations. The method has a low DNA input requirement and can detect low levels of mutant DNA in a large excess of normal DNA. These genes represent a minimal biomarker panel to which extra markers could be added to develop a highly sensitive diagnostic test for bladder cancer.     

Microbial Interference Between Indigenous Yeast and Lactobacilli in the Rodent Stomach

Indigenous yeasts grow in layers in the mucus on the secreting epithelium of the stomachs of some strains of rats and mice raised under conventional conditions. Likewise, indigenous lactobacilli appear in layers on the nonsecreting epithelium of the stomachs of rats and mice. The two microbial layers can coexist in the same animals. When I gave such rodents penicillin solution in the place of drinking water, the lactobacilli disappeared, and the yeast from the secreting epithelium colonized the nonsecreting epithelium within 24 hr. The yeast remained in layers on the nonsecreting, as well as the secreting epithelium, as long as penicillin was administered. There is no inflammatory reaction or any sign that the yeast invaded below the keratin layer. When the penicillin treatment was discontinued, within 5 to 8 days the indigenous lactobacilli again colonized the nonsecreting epithelium. Concomitantly the yeast was displaced from the keratinized tissue and once more could be found only on the secreting epithelium. Only 2 days were required, however, for the bacteria to recolonize the keratin layer and displace the yeast when the mice were given indigenous lactobacilli in pure culture immediately after the penicillin treatment was discontinued. The lactobacilli must displace the yeast from the nonsecreting epithelium by interfering either with multiplication of the yeast on the tissue or with attachment of the yeast cells to the keratin layer. This interference must proceed continuously during normal life since the yeast never populates the nonsecreting epithelium as long as the lactobacilli are present.     

Superovulation in the cow using estradiol 17beta or GnRH in conjunction with FSH-P

A study was designed to evaluate the superovulatory response in the cow when either estradiol 17beta or gonadotrophin releasing hormone (GnRH) was used in a superovulatory regimen with follicle stimulating hormone (FSH-P). Fifty-four cyclic crossbred females were superovulated in replicates between Days 8 and 12 of their cycle. All animals were treated with 28 mg of FSH-P in twice-daily decreasing doses, each receiving 500 mug cloprostenol (PGF) 48 h after initiation of treatment. Group 1 served as FSH-P controls, Group 2 received FSH-P and 400 mug of estradiol 17beta 36 h after PGF, and Group 3 received FSH-P and 250 mug GnRH 48 h after PGF. Inseminations with one vial of frozen semen were done at 12, 24 and 36 h after the onset of estrus. Ova/embryos were collected nonsurgically at Day 7 postestrus. Numbers of corpora lutea (CL) were recorded after palpation per rectum and the recovered ova and embryos were evaluated. All females were bled for endocrine examination. There were no differences in ovarian response among these treatments. Mean total ova/embryos collected in Group 3 was significantly higher than in Groups 1 or 2 (P < 0.05); however, no significant difference existed between groups in the mean numbers of fertilized or transferable embryos. Similarly, no significant differences existed between groups for recovery rate, fertilization rate, or percentage of transferable embryos. Serum estradiol levels were significantly higher at the expected end of ovulation in Group 2, and this tended to be associated with higher fertilization and transferable embryo rates. Furthermore, a significant positive correlation was found to exist between CL numbers and each of the ova/embryo parameters and the estradiol levels at estrus.     

Mitochondrial DNA in Candida pintolopesii, a yeast indigenous to the surface of the secreting epithelium of the murine stomach

Candida pintolopesii 108-1 is an indigenous yeast which colonizes the surface of the secreting gastric mucosa of mice. We have been exploring the aerobic respiratory capacities of this organism in reference to its capacity to colonize the stomach surface, an environment that could contain little oxygen for microbial growth. In this paper, we report mitochondrial DNA and membranes in cells of a strain of this yeast isolated from the gastric epithelium of a mouse and compare the findings with those made by other investigators in studies of Saccharomyces cerevisiae. Putative mitochondrial DNA was isolated from crude lysates of C. pintolopesii and S. cerevisiae as fluorescing bands in CsCl gradients containing 4',6-diamidino-2-phenylindole. The DNA from C. pintolopesii hybridized with a 32P-labeled DNA probe for the 21S rRNA gene encoded by mitochondrial DNA in S. cerevisiae. Postvital cell staining with 4',6-diamidino-2-phenylindole and rhodamine 123 revealed mitochondrial DNA and membranes, respectively, in the cytoplasm of intact C. pintolopesii cells. The staining patterns were generally similar to those reported for S. cerevisiae. Finally, structures similar to those reported to be mitochondria in electron micrographs of S. cerevisiae were seen in preparations of C. pintolopesii cells examined by transmission electron microscopy. These data confirm findings from studies of its respiratory capacity published earlier that a strain of C. pintolopesii isolated directly from its native habitat has functional mitochondria.     

Epidermal growth factor in blood

The presence of receptors for epidermal growth factor (EGF) in a wide variety of human tissues and also some tumours indicates an as yet undefined role for EGF and it is therefore necessary to know precise concentrations in blood and other fluids. We have investigated the occurrence of EGF in the circulation and found that in platelet rich plasma, EGF levels were 51 +/- 5 pmol/l (mean +/- S.E.M., n = 6) while in platelet poor plasma levels were 2.9 +/- 0.9 pmol/1. In contrast, serum EGF was 37 +/- 7 pmol/l if separated at 30 min and rose to 117 +/- 5 pmol/l if separated at 270 min. Gel chromatography showed that all residual EGF immunoreactivity in platelet poor plasma resided in the high molecular weight form thought to be non biologically active. In serum, delay in separation resulted in an increase in the proportion of EGF immunoreactivity co-eluting with EGF standard. These results suggest that EGF in the circulation is associated with platelets and that the process of blood coagulation leads to release of free EGF.     

Lipoteichoic acids in Lactobacillus strains that colonize the mouse gastric epithelium.

Extracts of cells of 22 strains of Lactobacillus species, and of fluids from cultures in a defined medium of two of the strains, were assayed by hemagglutination inhibition for lipoteichoic acids. A total of 10 of the preparations gave positive tests for the acids, including those from eight strains known to adhere to the keratinized squamous epithelium of the mouse stomach. These findings are consistent with an hypothesis that lactobacilli colonize the epithelial surface via adhesive interaction with the keratinized cells mediated by macromolecular complexes containing lipoteichoic acids.     

Estrogen induced synthesis of specific proteins in human breast cancer cells

Human breast cancer cells in tissue culture (MCF-7) were pretreated with the antiestrogen nafoxidine to arrest cellular proliferation and then were given estradiol to release this block and stimulate DNA synthesis and cell division. During this period of growth stimulation intracellular proteins, labeled by a double isotope method, were analyzed on SDS-polyacrylamide gel electrophoresis. Estradiol directly increases the rates of synthesis of specific proteins which migrate on SDS-gels at molecular weights of 24,000 and 36,000. Nafoxidine-pretreatment alone does not induce these same proteins, and no changes in the rates of specific protein synthesis occur in cells grown on control medium for the same length of time as on estradiol. Induced synthesis of these proteins is observed only during the period of estrogen stimulation of cell proliferation following pretreatment with nafoxidine. We do not detect induction when cells are incubated with estradiol without antiestrogen-pretreatment. Since rescue of antiestrogen growth inhibition is also the only condition under which MCF-7 cell division can be reproducibly stimulated by estrogen, these proteins may be related to estrogen effects on cellular proliferation.