An archaeal family-B DNA polymerase variant able to replicate past DNA damage: occurrence of replicative and translesion synthesis polymerases within the B family

A mutant of the high fidelity family-B DNA polymerase from the archaeon Thermococcus gorgonarius (Tgo-Pol), able to replicate past DNA lesions, is described. Gain of function requires replacement of the three amino acid loop region in the fingers domain of Tgo-Pol with a longer version, found naturally in eukaryotic Pol zeta (a family-B translesion synthesis polymerase). Inactivation of the 3'–5' proofreading exonuclease activity is also necessary. The resulting Tgo-Pol Z1 variant is proficient at initiating replication from base mismatches and can read through damaged bases, such as abasic sites and thymine photo-dimers. Tgo-Pol Z1 is also proficient at extending from primers that terminate opposite aberrant bases. The fidelity of Tgo-Pol Z1 is reduced, with amarked tendency tomake changes at G:C base pairs. Together, these results suggest that the loop region of the fingers domain may play a critical role in determining whether a family-B enzyme falls into the accurate genome-replicating category or is an errorprone translesion synthesis polymerase. Tgo-Pol Z1 may also be useful for amplification of damaged DNA

Contextual organismality: Beyond pattern to process in the emergence of organisms

Biologists have taken the concept of organism largely for granted. However, advances in the study of chimerism, symbiosis, bacterial-eukaryote associations, and microbial behavior have prompted a redefinition of organisms as biological entities exhibiting low conflict and high cooperation among their parts. This expanded view identifies organisms in evolutionary time. However, the ecological processes, mechanisms, and traits that drive the formation of organisms remain poorly understood. Recognizing that organismality can be context dependent, we advocate elucidating the ecological contexts under which entities do or do not act as organisms. Here we develop a "contextual organismality" framework and provide examples of entities, such as honey bee colonies, tumors, and bacterial swarms, that can act as organisms under specific life history, resource, or other ecological circumstances. We suggest that context dependence may be a stepping stone to the development of increased organismal unification, as the most integrated biological entities generally show little context dependence. Recognizing that organismality is contextual can identify common patterns and testable hypotheses across different entities. The contextual organismality framework can illuminate timeless as well as pressing issues in biology, including topics as disparate as cancer emergence, genomic conflict, evolution of symbiosis, and the role of the microbiota in impacting host phenotype.John Templeton FoundationVersion of record online: 27 October 2016; published open access.This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Identification of putative methanol dehydrogenase (moxF) structural genes in methylotrophs and cloning of moxF genes from Methylococcus capsulatus bath and Methylomonas albus BG8

An open-reading-frame fragment of a Methylobacterium sp. strain AM1 gene (moxF) encoding a portion of the methanol dehydrogenase structural protein has been used as a hybridization probe to detect similar sequences in a variety of methylotrophic bacteria. This hybridization was used to isolate clones containing putative moxF genes from two obligate methanotrophic bacteria, Methylococcus capsulatus Bath and Methylomonas albus BG8. The identity of these genes was confirmed in two ways. A T7 expression vector was used to produce methanol dehydrogenase protein in Escherichia coli from the cloned genes, and in each case the protein was identified by immunoblotting with antiserum against the Methylomonas albus methanol dehydrogenase. In addition, a moxF mutant of Methylobacterium strain AM1 was complemented to a methanol-positive phenotype that partially restored methanol dehydrogenase activity, using broad-host-range plasmids containing the moxF genes from each methanotroph. The partial complementation of a moxF mutant in a facultative serine pathway methanol utilizer by moxF genes from type I and type X obligate methane utilizers suggests broad functional conservation of the methanol oxidation system among gram-negative methylotrophs

A mechanistic explanation linking adaptive mutation, niche change, and fitness advantage for the Wrinkly Spreader

Experimental evolution studies have investigated adaptive radiation in static liquid microcosms using the environmental bacterium Pseudomonas fluorescens SBW25. In evolving populations a novel adaptive mutant known as the Wrinkly Spreader arises within days having significant fitness advantage over the ancestral strain. A molecular investigation of the Wrinkly Spreader has provided a mechanistic explanation linking mutation with fitness improvement through the production of a cellulose-based biofilm at the air-liquid interface. Colonisation of this niche provides greater access to oxygen, allowing faster growth than that possible for non-biofilm—forming competitors located in the lower anoxic region of the microcosm. Cellulose is probably normally used for attachment to plant and soil aggregate surfaces and to provide protection in dehydrating conditions. However, the evolutionary innovation of the Wrinkly Spreader in static microcosms is the use of cellulose as the matrix of a robust biofilm, and is achieved through mutations that deregulate multiple diguanylate cyclases leading to the over-production of cyclic-di-GMP and the stimulation of cellulose expression. The mechanistic explanation of the Wrinkly Spreader success is an exemplar of the modern evolutionary synthesis, linking molecular biology with evolutionary ecology, and provides an insight into the phenomenal ability of bacteria to adapt to novel environments

Big Dreams for Small Creatures: Ilana and Eugene Rosenberg’s path to the Hologenome Theory

A biographical sketch of the Hologenome Theory

Electroactive biofilms: new means for electrochemistry

This work demonstrates that electrochemical reactions can be catalysed by the natural biofilms that form on electrode surfaces dipping into drinking water or compost. In drinking water, oxygen reduction was monitored with stainless steel ultra-microelectrodes under constant potential electrolysis at )0.30 V/SCE for 13 days. 16 independent experiments were conducted in drinking water, either pure or with the addition of acetate or dextrose. In most cases, the current increased and reached 1.5–9.5 times the initial current. The current increase was attributed to biofilm forming on the electrode in a similar way to that has been observed in seawater. Epifluorescence microscopy showed that the bacteria size and the biofilm morphology depended on the nutrients added, but no quantitative correlation between biofilm morphology and current was established. In compost, the oxidation process was investigated using a titanium based electrode under constant polarisation in the range 0.10–0.70 V/SCE. It was demonstrated that the indigenous micro-organisms were responsible for the current increase observed after a few days, up to 60 mA m)2. Adding 10 mM acetate to the compost amplified the current density to 145 mA m)2 at 0.50 V/SCE. The study suggests that many natural environments, other than marine sediments, waste waters and seawaters that have been predominantly investigated until now, may be able to produce electrochemically active biofilm

Biological Individuals

The impressive variation amongst biological individuals generates many complexities in addressing the simple-sounding question what is a biological individual? A distinction between evolutionary and physiological individuals is useful in thinking about biological individuals, as is attention to the kinds of groups, such as superorganisms and species, that have sometimes been thought of as biological individuals. More fully understanding the conceptual space that biological individuals occupy also involves considering a range of other concepts, such as life, reproduction, and agency. There has been a focus in some recent discussions by both philosophers and biologists on how evolutionary individuals are created and regulated, as well as continuing work on the evolution of individuality

Partial quantification of pigments extracted from the zooxanthellate octocoral Sinularia flexibilis at varying irradiances

Chlorophyll-a (chl-a) and carotenoid pigments of the zooxanthellate octocoral Sinularia flexibilis were analyzed using high performance liquid chromatography following exposure to three light intensities for over 30 days. From the coral fragments located at different light intensities, a total carotenoid of >41 µg g-1 dry weight, including peridinin, xanthophylls (likely diadinoxanthin + diatoxanthin), and chl-a as the most abundant pigments, with minor contents of astaxantin and ß-carotene were detected. The whole content of chl-a weighed 5 µg g-1 dry weight in all coral colonies. Chl-a and carotenoids contributed 11.2% and 88.2%, respectively, to all pigments detected, and together accounted for 99.4% of the total pigments present. The highest contents of carotenoids and chl-a was observed in the coral grafts placed in an irradiance of 100 µmol quanta m-2 s-1; they showed lower ratios of total carotenoids: chl-a compared to those exposed to 400 µmol quanta m-2 s-1 after >30 days of incubation. The ratios of peridinin and xanthophylls with respect to chl-a from the colonies at 400 µmol quanta m-2 s-1 were approximately double those observed at irradiances of 100 and 200 µmol quanta m-2 s-1. Partial quantification of pigments in this study showed that the carotenoids of S. flexibilis showed a decrease at irradiances above 100 µmol quanta m-2 s-1, with the exception of an increase in ß-carotene at 200 µmol quanta m-2 s-1

Influence of Thyme and Juniper on the Microbiological Properties of Pork Brisket

The aim of the work is to determine an influence of non-traditional mixtures of spicy-aromatic plants of thyme and juniper, their essential oils and alcohol extracts on the course of microbiological processes in pork brisket. Pork brisket was an experimental sample. It was added with black pepper, thyme and juniper, in the dry condition, as essential oils and alcohol extracts. Pork brisket, added with dry plants, essential oils, extracts of black and fragrant pepper, was taken as a control. According to the microbiological studies, it was established, that an exceed of the standard index of the content of mesophilic-aerobic and facultative anaerobic microorganisms (more than 1,0×103 g/CCU) takes place in brisket samples with dry black pepper. And also in samples with thyme and juniper in ratios 0,9:0,7:0,2 and 0,9:0,6:0,3. An exceed of nMAFAM index is also fixed in experiments using essential oils of these spices. It was established, that after 80 min of the experiment, these mixtures remain resistant to spoilage by 20 min longer comparing with using dry black and fragrant pepper. Most intense antibacterial properties relative to the development of microorganisms were observed in experimental samples. It is noticeable in a sample with using dry comminuted spices thyme and juniper in ratios 0,9:0,8:0,1. The use of spicy-aromatic plants of thyme and juniper allow to increase the storage term of ready products