Analysis of Barry Hall\u27s Research of the E. coli ebg Operon: Understanding the Implications for Bacterial Adaptation to Adverse Environments

Much research has been done on the ebg operon of the bacterium Escherichia coli over the last 30 years. Although the function of the ebg operon is still unknown, it has been observed that specific mutations within this operon enable the bacterium to metabolize lactose sufficiently to allow growth. Interestingly, this growth occurs in a lacZ- genotype (gene for β-galactosidase in the lac operon). Thus, this gene has been referred to as an “evolved β-galactosidase,” and has been widely accepted as an example of “evolution in action.” Under these cultivation conditions, the ebg operon appears to harbor adaptive mutations. Mutations (at codons 92 and 977) in the ebgA gene (which codes for ebg β-galactosidase) occur consistently when an E. coli lacZ- population undergoes carbon starvation in the presence of lactose. These are the only mutations observed in the ebgA gene and these particular mutations are not found when the bacteria are subjected to different adverse environmental conditions. Mutations are also found in other genes suggesting a mechanism which has affects on the entire genome. Several models have been proposed to explain this phenomenon. Hall’s work needs critical evaluation. Mutations in the Ebg system are clearly not an example of evolution but mutation and natural selection allowing for adaptation to the environment. Several possibilities for the function of the Ebg system are suggested. In addition, there is an assessment of the likelihood of these mutations in the ebg operon occurring in a natural setting. An implication of this research is an understanding that adaptive mutation makes “limited” changes which severely restrict its use as a mechanism for evolution. Adaptive mutations can readily fit within a creation model where adaptive mechanisms are a designed feature of bacteria. Further understanding of these mutations in the ebg operon may help the development of a creation model for adaptation of bacterial populations in response to the adverse environmental conditions in a post-Fall, post-Flood world

A Creationist Perspective of Beneficial Mutations in Bacteria

Mutations alter the nucleotide sequence of the DNA. They may affect the organism’s phenotype, which can play a key role in bacterial adaptation and transformation to changing environments. Some of these mutations even appear to be beneficial to the organism. However, creationists have tended to offer an inconsistent or incomplete perspective of “beneficial mutations” within a creation framework. This includes the frequent denial that mutations can ever provide a beneficial phenotype, and the concept that “beneficial mutations” are merely an evolutionist exaggeration. In bacteria, a wide range of mutations can be shown to provide a beneficial phenotype to the cell. These benefits are often of sufficient phenotypic affect that they can undergo strong positive selection. But, the benefits are generally temporary and limited. Some common examples of beneficial mutations are those involved in bacterial antibiotic resistance. These mutations potentially enable the bacterium to survive exposure to various antibiotics, but the resistance results from loss or reduction of pre-existing activities such as enzymatic, regulatory, or transport systems. Bacteria also can undergo adaptive mutation; a phenomenon used by bacteria to survive very specific stressful conditions. The exact mechanism is controversial because some results suggest a directed mutation specifically enabling adaptation to the environment, but at a mutation rate higher than random mutations would produce. Various mutations have also been found that enable bacteria to survive temporary exposure to high temperatures or starvation. Such mutations usually involve loss of certain sigma factors, reduction of DNA repair, or loss of specific regulatory controls. Other examples include several subpopulations of mutant strains of bacteria obtained over a period of up to 20,000 generations. These mutants have a greater “fitness” than the wild-type strain. However, analysis showed that most contained deletion mutations in various genes. Each of these examples, as well as numerous others, involves certain environmental conditions that make these mutations phenotypically beneficial. However, these mutations frequently eliminate or reduce pre-existing cellular systems and functions. This has been referred to as antagonistic pleiotropy; meaning the cell experiences a trade-off where a temporary benefit for surviving one environmental condition is provided at the expense of systems used for other environments. If the environmental conditions change, the mutation usually becomes less beneficial and perhaps even detrimental. Hence, these mutations do not provide a genetic mechanism that accounts for the origin of biological systems or functions. Rather, they require the prior existence of the targeted cellular systems. As such, beneficial mutations of bacteria fit concisely within a creation model where (a) biological systems and functions were fully formed at creation, (b) subsequent mutations can provide conditional benefits that enable the organism to survive harsh post-Fall conditions even though the mutation is generally degenerative, and (c) most bacteria need the ability to rapidly adapt to ever changing environments and food sources

Transcription restores DNA repair to heterochromatin, determining regional mutation rates in cancer genomes

Somatic mutations in cancer are more frequent in heterochromatic and late-replicating regions of the genome. We report that regional disparities in mutation density are virtually abolished within transcriptionally silent genomic regions of cutaneous squamous cell carcinomas (cSCCs) arising in an XPC(-/-) background. XPC(-/-) cells lack global genome nucleotide excision repair (GG-NER), thus establishing differential access of DNA repair machinery within chromatin-rich regions of the genome as the primary cause for the regional disparity. Strikingly, we find that increasing levels of transcription reduce mutation prevalence on both strands of gene bodies embedded within H3K9me3-dense regions, and only to those levels observed in H3K9me3-sparse regions, also in an XPC-dependent manner. Therefore, transcription appears to reduce mutation prevalence specifically by relieving the constraints imposed by chromatin structure on DNA repair. We model this relationship among transcription, chromatin state, and DNA repair, revealing a new, personalized determinant of cancer risk

Should Histologic Grade Be Incorporated into the TNM Classification System for Small (T1, T2) Node-Negative Breast Adenocarcinomas?

Prognosis of invasive ductal carcinoma (IDC) strongly correlates with tumor grade as determined by Nottingham combined histologic grade. While reporting grade as low grade/favorable (G1), intermediate grade/moderately favorable (G2), and high grade/unfavorable (G3) is recommended by American Joint Committee on Cancer (AJCC) staging system, existing TNM (Primary Tumor/Regional Lymph Nodes/Distant Metastasis) classification does not directly incorporate these data. For large tumors (T3, T4), significance of histologic grade may be clinically moot as those are nearly always candidates for adjuvant therapy. However, for small (T1, T2) node-negative (N0) tumors, grade may be clinically relevant in influencing treatment decisions, but data on outcomes are sparse and controversial. This retrospective study analyzes clinical outcome in patients with small N0 IDC on the basis of tumor grade. Our results suggest that the grade does not impact clinical outcome in T1N0 tumors. In T2N0 tumors, however, it might be prognostically significant and relevant in influencing decisions regarding the need for additional adjuvant therapy and optimal management

Automating Grammar Comparison

We consider from a practical perspective the problem of checking equivalence of context-free grammars. We present techniques for proving equivalence, as well as techniques for finding counter-examples that establish non-equivalence. Among the key building blocks of our approach is a novel algorithm for efficiently enumerating and sampling words and parse trees from arbitrary context-free grammars; the algorithm supports polynomial time random access to words belonging to the grammar. Furthermore, we propose an algorithm for proving equivalence of context-free grammars that is complete for LL grammars, yet can be invoked on any context-free grammar, including ambiguous grammars. Our techniques successfully find discrepancies between different syntax specifications of several real-world languages, and are capable of detecting fine-grained incremental modifications performed on grammars. Our evaluation shows that our tool improves significantly on the existing available state of the art tools. In addition, we used these algorithms to develop an online tutoring system for grammars that we then used in an undergraduate course on computer language processing. On questions involving grammar constructions, our system was able to automatically evaluate the correctness of 95% of the solutions submitted by students: it disproved 74% of cases and proved 21% of the

Innate Immune Activation by Checkpoint Inhibition in Human Patient-Derived Lung Cancer Tissues

Although Pembrolizumab-based immunotherapy has significantly improved lung cancer patient survival, many patients show variable efficacy and resistance development. A better understanding of the drug’s action is needed to improve patient outcomes. Functional heterogeneity of the tumor microenvironment (TME) is crucial to modulating drug resistance; understanding of individual patients’ TME that impacts drug response is hampered by lack of appropriate models. Lung organotypic tissue slice cultures (OTC) with patients’ native TME procured from primary and brain-metastasized (BM) non-small cell lung cancer (NSCLC) patients were treated with Pembrolizumab and/or beta-glucan (WGP, an innate immune activator). Metabolic tracing with 13C6-Glc/13C5,15N2-Gln, multiplex immunofluorescence, and digital spatial profiling (DSP) were employed to interrogate metabolic and functional responses to Pembrolizumab and/or WGP. Primary and BM PD-1+ lung cancer OTC responded to Pembrolizumab and Pembrolizumab + WGP treatments, respectively. Pembrolizumab activated innate immune metabolism and functions in primary OTC, which were accompanied by tissue damage. DSP analysis indicated an overall decrease in immunosuppressive macrophages and T cells but revealed microheterogeneity in immune responses and tissue damage. Two TMEs with altered cancer cell properties showed resistance. Pembrolizumab or WGP alone had negligible effects on BM-lung cancer OTC but Pembrolizumab + WGP blocked central metabolism with increased pro-inflammatory effector release and tissue damage. In-depth metabolic analysis and multiplex TME imaging of lung cancer OTC demonstrated overall innate immune activation by Pembrolizumab but heterogeneous responses in the native TME of a patient with primary NSCLC. Metabolic and functional analysis also revealed synergistic action of Pembrolizumab and WGP in OTC of metastatic NSCLC

Seminar on Evidence and Trial Practice

Outlines of speaker presentations offered during a series of one day seminars on evidence and trial practice offered by UK/CLE in late 1987-early 1988

The fate of steroid estrogens: Partitioning during wastewater treatment and onto river sediments

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ 2010 Springer Science+Business Media B.V.The partitioning of steroid estrogens in wastewater treatment and receiving waters is likely to influence their discharge to, and persistence in, the environment. This study investigated the partitioning behaviour of steroid estrogens in both laboratory and field studies. Partitioning onto activated sludge from laboratory-scale Husmann units was rapid with equilibrium achieved after 1 h. Sorption isotherms and Kd values decreased in the order 17α-ethinyl estradiol > 17α-estradiol > estrone > estriol without a sorption limit being achieved (1/n >1). Samples from a wastewater treatment works indicated no accumulation of steroid estrogens in solids from primary or secondary biological treatment, however, a range of steroid estrogens were identified in sediment samples from the River Thames. This would indicate that partitioning in the environment may play a role in the long-term fate of estrogens, with an indication that they will be recalcitrant in anaerobic conditions.EPSR

A critical review of the formation of mono- and dicarboxylated metabolic intermediates of alkylphenol polyethoxylates during wastewater treatment and their environmental significance

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ 2010 Taylor & Francis.Alkylphenoxyacetic acids, the metabolic biodegradation products of alkylphenol ethoxylates, are commonly found in wastewaters and sewage effluents. These persistent hydrophilic derivatives possess intrinsic estrogenic activity, which can mimic natural hormones. Their concentrations increase through the sewage treatment works as a result of biodegradation and biotransformation, and when discharged can disrupt endocrine function in fish. These acidic metabolites represent the dominant alkylphenolic compounds found in wastewater effluent and their presence is cause for concern as, potentially, through further biotransformation and biodegradation, they can act as sources of nonylphenol, which is toxic and estrogenic. The authors aim to assess the mechanisms of formation as well as elimination of alkylphenoxyacetic acids within conventional sewage treatment works with the emphasis on the activated sludge process. In addition, they evaluate the various factors influencing their degradation and formation in laboratory scale and full-scale systems. The environmental implications of these compounds are considered, as is the need for tertiary treatment processes for their removal

Computational Cancer Biology: An Evolutionary Perspective

ISSN:1553-734XISSN:1553-735