Optimizing the strain engineering process for industrial-scale production of bio-based molecules

Biomanufacturing could contribute as much as ${\$}$30 trillion to the global economy by 2030. However, the success of the growing bioeconomy depends on our ability to manufacture high-performing strains in a time- and cost-effective manner. The Design-Build-Test-Learn (DBTL) framework has proven to be an effective strain engineering approach. Significant improvements have been made in genome engineering, genotyping, and phenotyping throughput over the last couple of decades that have greatly accelerated the DBTL cycles. However, to achieve a radical reduction in strain development time and cost, we need to look at the strain engineering process through a lens of optimizing the whole cycle, as opposed to simply increasing throughput at each stage. We propose an approach that integrates all 4 stages of the DBTL cycle and takes advantage of the advances in computational design, high-throughput genome engineering, and phenotyping methods, as well as machine learning tools for making predictions about strain scale-up performance. In this perspective, we discuss the challenges of industrial strain engineering, outline the best approaches to overcoming these challenges, and showcase examples of successful strain engineering projects for production of heterologous proteins, amino acids, and small molecules, as well as improving tolerance, fitness, and de-risking the scale-up of industrial strains.

A new paradigm (Westphal-Paradigm) to study the neural correlates of panic disorder with agoraphobia

Agoraphobia (with and without panic disorder) is a highly prevalent and disabling anxiety disorder. Its neural complexity can be characterized by specific cues in fMRI studies. Therefore, we developed a fMRI paradigm with agoraphobia-specific stimuli. Pictures of potential agoraphobic situations were generated. Twenty-six patients, suffering from panic disorder and agoraphobia, and 22 healthy controls rated the pictures with respect to arousal, valence, and agoraphobia-related anxiety. The 96 pictures, which discriminated best between groups were chosen, split into two parallel sets and supplemented with matched neutral pictures from the International Affective Picture System. Reliability, criterion, and construct validity of the picture set were determined in a second sample (44 patients, 28 controls). The resulting event-related "Westphal-Paradigm" with cued and uncued pictures was tested in a fMRI pilot study with 16 patients. Internal consistency of the sets was very high; parallelism was given. Positive correlations of picture ratings with Mobility Inventory and Hamilton anxiety scores support construct validity. FMRI data revealed activations in areas associated with the fear circuit including amygdala, insula, and hippocampal areas. Psychometric properties of the Westphal-Paradigm meet necessary quality requirements for further scientific use. The paradigm reliably produces behavioral and fMRI patterns in response to agoraphobia-specific stimuli. To our knowledge, it is the first fMRI paradigm with these properties. This paradigm can be used to further characterize the functional neuroanatomy of panic disorder and agoraphobia and might be useful to contribute data to the differentiation of panic disorder and agoraphobia as related, but conceptually different clinical disorders.

Preliminary validation of two novel immunoassays for detecting VEGF in human and mouse plasma using single molecule counting technology

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Background: Growth in biomarkers as therapeutic targets and as surrogate markers for efficacy presents a need for increasingly sensitive immunoassays to expand biomarker applicability. Improved immunoassays will provide: (1) better evaluation and validation of new drug candidates, (2) better matching of patients to new therapies, (3) accelerated drug approval (4) earlier diagnosis of at-risk patients, and (5) a deeper understanding of cancer biology. Towards this end, Singulex has developed two ultra- sensitive VEGF Immunoassays for human and mouse vascular endothelial growth factor (VEGF). Here we report the preliminary validation of these two novel assays. Methods: Two novel assays were developed with the Erenna Immunoassay System for detecting VEGF: human (hVEGF) and mouse (mVEGF). Analytical sensitivity, cross-reactivity and precision were determined and compared to an ELISA based VEGF assay. Both the Singulex assay and ELISA assay were used to test a range of specimen types (plasma, cell lysates, conditioned media, and tissue specimens) from humans and mice. Preliminary assays with human plasma and tissue specimens were conducted to compare hVEGF levels between normal and breast cancer samples. Results: The Singulex hVEGF assay had an LOD of 0.1 pg/mL, an LLOQ of 0.3 pg/mL, and 84–107% spike recovery; 90X more sensitive than the ELISA assay. Human VEGF concentrations were quantified in all specimens tested compared to the ELISA, which quantified VEGF in only 8% of plasma samples, but all of the cell lysate samples. The Singulex mVEGF assay had an LOD of 3.5 pg/mL, LLOQ of 5 pg/mL, and 68–111% spike recovery; 3X more sensitive than the ELISA assay. Cross-reactivity for the two assays was minimal for all specimen types tested, except for human plasma samples where the mVEGF assay demonstrated 80–100% CR. Conclusions: We show that the Singulex hVEGF and mVEGF Immunoassays can detect VEGF at or below pg/mL levels, and can effectively quantify VEGF levels in plasma, cell lysates, conditioned media, and tissue samples from mice and humans. These novel assays are an important tool when used to assess tumor and normal breast cancer tissue and plasma.

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Development of ultra-sensitive single molecule immunoassays for the intracellular kinases Akt1/pAkt1 and Erk2/pErk2 for small tissue studies

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Background: The Ras/Raf/MEK/ERK and PI3K/PTEN/AKT kinase cascades are critical pathways in malignant transformation, tumor progression and multi-drug resistance (MDR) in human cancers. Expression and genetic studies have contributed much to our understanding of this role, but further clinical investigations at the post-transcriptional level are necessary. Towards this end, Singulex has developed single molecule immunoassays for total Akt1, pAkt1, total Erk2 and pErk2 utilizing the Erenna Immunoassay System for use in small tissue studies and clinical trials. Methods: Analytical sensitivity, inter- assay precision, linearity and specificity were determined and compared to corresponding ELISA assays. Novel assays were tested on lysates from a variety of commonly utilized cell lines in cancer studies: MCF-7, PBMC, Jurkat, HeLa, and NIH3T3 cells. Results: All four novel assays were significantly more sensitive than the ELISA assay method based upon sample endpoint dilutions. Acceptable precision (<20%CV) was demonstrated for the Akt1/pAkt1 assays in PBMC lysates and for the Erk2/pErk2 assays in MCF-7, HeLa and NIH3T3 lysates. The LLoQ of the Akt1/pAkt1 assay in Jurkat lysates was sufficient to quantify Akt1/pAkt1 from as few as 10–20 cells. Based upon a typical 1mm needle biopsy, this is sufficient to quantify Akt1/pAkt1 from less than 1/1000th of that biopsy. Conclusions: We show that the Singulex Akt1, pAkt1, Erk2 and pErk2 assays are over 50 fold more sensitive than currently available ELISA assays, and specifically quantify analyte in a variety of cell lysates. We have further demonstrated that the Akt1/pAkt1 assay can quantify from as little as 1/1000th of a typical needle biopsy. Thus, these novel assays greatly improve upon pre- existing technology, providing a new tool for clinical trials investigating Ras/Raf/MEK/ERK and PI3K/PTEN/AKT pathways previously limited by ELISA sensitivity.

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Genetic and physical localization of the soybean Rpg1-b disease resistance gene reveals a complex locus containing several tightly linked families of NBS-LRR genes

Alleles or tightly linked genes at the soybean (Glycine max L. Merr.) Rpg1 locus confer resistance to strains of Pseudomonas syringae pv. glycinea that express the avirulence genes avrB or avrRpm1. We have previously mapped Rpg1-b (the gene specific for avrB) to a cluster of resistance genes (R genes) with diverse specificities in molecular linkage group F. Here, we describe the high-resolution physical and genetic mapping of Rpg1-b to a 0.16-cM interval encompassed by two overlapping BAC clones spanning approximately 270 kilobases. Rpg1-b is part of a complex locus containing numerous genes related to previously characterized coiled coil-nucleotide binding site-leucine rich repeat (CC-NBS-LRR)-type R genes that are spread throughout this region. Phylogenetic and Southern blot analyses group these genes into four distinct subgroups, some of which are conserved in the common bean, Phaseolus vulgaris, indicating that this R gene cluster may predate the divergence of Phaseolus and Glycine. Members from different subgroups are physically intermixed and display a high level of polymorphism between soybean cultivars, suggesting that this region is rearranging at a high frequency. At least five CC-NBS-LRR-type genes cosegregate with Rpg1-b in our large mapping populations.

O6-Alkylguanine-DNA alkyltransferase in normal colon tissue and colon cancer

O6-Alkylguanine-DNA alkyltransferase (AGT) is a DNA repair protein that reverses alkylation damage produced by chloroethylnitrosoureas and is a major determinant of cellular resistance to adjuvant chemotherapy with these drugs. AGT activity was measured in 119 samples from 69 patients, including normal, tumor, and diseased tissue, and 42 patients in which both normal and tumor tissue were assayed. The activity varied among individuals, but there was no statistically significant difference in average AGT activity among tumor, normal, and diseased tissue, or between men and women, or between young and old patients (< 70 or > 70 years). Few (3/49) tumor samples showed an absence of AGT activity (Mer- phenotype). The results indicate that nearly all colon cancers have significant AGT activity, and adjuvant chloroethylnitrosoureas chemotherapy must be modified, perhaps by the use of AGT biochemical modulators, to overcome this natural drug resistance.

O6-methylguanine-DNA methyltransferase in normal and malignant tissue of the breast

An important component of high-dose chemotherapy/autologous bone marrow support regimens for adjuvant treatment of breast cancer is carmustine. Preclinical studies have shown that the level of the DNA repair protein O6-methylguanine-DNA methyltransferase is correlated with the resistance of cultured human tumor cells to this drug, but little is known about transferase levels of breast tissue in vivo. We measured the DNA repair activity in 80 tissue samples from 65 patients, including normal, abnormal, benign, and malignant specimens. Wide interindividual variations was observed and average transferase levels were similar in normal and benign tissue. However, transferase levels were significantly elevated in stage I-IV disease. In addition, the frequency of samples with no detectable transferase was greatly reduced in this malignant group, and transferase was positively correlated with the presence of positive nodes, a marker for disease progression. In contrast, transferase levels were not correlated with age or estrogen receptor status, and the levels in normal tissue did not vary between patients with benign or malignant disease. These results suggest that this DNA repair activity may be increased in breast cancer relative to normal tissue and encourage further study of the predictive value of transferase measurements in high-dose chemotherapy/autologous bone marrow transplant for breast cancer.

Management of anorectal horseshoe abscess and fistula

Over a 10-year period 69 patients were treated consecutively for posterior and anterior horseshoe abscesses and fistulas. Fifty-nine patients had posterior and ten had anterior abscesses or fistulas. There were 52 patients with acute abscess. Treatment consisted of incision and drainage, incision and drainage with primary fistulotomy, incision and drainage with primary fistulotomy and counter-drainage, and incision and drainage with insertion of seton. Seventeen patients with chronic fistulas were treated by primary fistulotomy with curettage, or incision and drainage with insertion of seton. Patients were followed from three months to ten years with a mean follow-up of three years. No incidences of incontinence were reported in this series. The overall rate of recurrence was 18 percent, and included only patients with posterior abscesses and fistulas. Recurrence was related to the failure to maintain prolonged drainage in the midline after primary fistulotomy. The use of seton for delayed fistulotomy appears to promote wound drainage and precludes premature wound closure. More liberal use of the seton in the treatment of horseshoe abscesses and fistulas is advocated.

Cognitive mapping and elderly adults: verbal and location memory for urban landmarks

This study provides a real-world memory task that extends the ecological validity of previous research on aging and spatial memory. Elderly individuals were found to have less accurate verbal recall of urban landmarks and location memory for landmarks than younger adults. In addition to these quantitative differences in environmental cognition, qualitative aspects of the data were explored. In order to explain the poorer memory performance of elderly adults, participants' use of a geographically based, organizational mnemonic was examined. Furthermore, discriminant analysis revealed that the elderly relied more than younger adults on certain building attributes for memory of urban landmarks. These building attributes include: high public use, high symbolic significance, naturalness of surroundings, direct access to streets, and unique architectural style.