Reply to comment on the paper by Davies et al. “Resolving MISS conceptions and misconceptions: A geological approach to sedimentary surface textures generated by microbial and abiotic processes”

We thank Noffke (2017) for her comment and for providing an opportunity to clarify our classification of “sedimentary surface textures”. We accord great credit to Dr. Noffke and other dedicated researchers whose detailed work has brought microbially induced sedimentary structures (MISS) to the widespread attention of geoscientists. However, we stand by our assertion that attributing structures observed in practical field and laboratory studies to processes of formation is much more problematic than Noffke (2017) indicates. Indeed, points in the Comment confirm the need for a classification system that categorises the degree of certainty attributed to a given interpretation. We stress that our paper was not designed as a critique of previous studies of MISS but rather was designed to encourage a reasonable assessment of uncertainty in assigning sedimentary surface textures to physical processes or to MISS

Northern Bobwhite Population Structure and Diversity in Texas and the Great Plains

Many northern bobwhite (Colinus virginianus) populations have been experiencing severe declines. This decline is of concern to wildlife biologists, landowners, and legislators due to the popularity of this species as a game bird. Previous molecular genetic analyses for populations inhabiting intact habitats in South Texas indicate the northern bobwhite population in this region is genetically diverse with low population structure. W[e] assessed whether landscape affects the population structure and diversity for northern bobwhite in Texas and the Great Plains. We extracted DNA from hunter-harvested northern bobwhites from 19 sites in South Texas from 2004 to 2010. We analyzed 7 microsatellites (Quail 5, 8, 9, 10, 11, 12, and 15). We used FST to measure genetic structure and AMOVA for genetic variation. We built 3 matrices to compare the genetic structure with the landscape. Geographic distances (km) between sample locations were ascertained using Google Earth. A matrix of barriers incorporated large water bodies and highways. We used the Biologist Ranking Information from the National Bobwhite Conservation Initiative for the third matrix to identify the number of different habitat patches a quail would need to cross from ranch to ranch. These matrices were compared to the genetic structure (pairwise FST), using Mantel tests with 10,000 permutations. We used partial Mantel tests to test the correlation of pairwise FST to combinations of distance and barriers, distance and habitat, and barriers and habitat. Overall FST was \u3c 0.01, suggesting low levels of population differentiation and AMOVA revealed most variation was within individuals. All Mantel tests had a positive correlation with genetic differentiation; however, barriers appear to be important factors for the observed genetic patterns

Resolving MISS conceptions and misconceptions: A geological approach to sedimentary surface textures generated by microbial and abiotic processes

The rock record contains a rich variety of sedimentary surface textures on siliciclastic sandstone, siltstone and mudstone bedding planes. In recent years, an increasing number of these textures have been attributed to surficial microbial mats at the time of deposition, resulting in their classification as microbially induced sedimentary structures, or MISS. Research into MISS has developed at a rapid rate, resulting in a number of misconceptions in the literature. Here, we attempt to rectify these MISS misunderstandings. The first part of this paper surveys the stratigraphic and environmental range of reported MISS, revealing that contrary to popular belief there are more reported MISS-bearing rock units of Phanerozoic than Precambrian age. Furthermore, MISS exhibit a pan-environmental and almost continuous record since the Archean. Claims for the stratigraphic restriction of MISS to intervals prior to the evolution of grazing organisms or after mass extinction events, as well as claims for the environmental restriction of MISS, appear to result from sampling bias. In the second part of the paper we suggest that raised awareness of MISS has come at the cost of a decreasing appreciation of abiotic processes that may create morphologically similar features. By introducing the umbrella term ‘sedimentary surface textures’, of which MISS are one subset, we suggest a practical methodology for classifying such structures in the geological record. We illustrate how elucidating the formative mechanisms of ancient sedimentary surface textures usually requires consideration of a suite of sedimentological evidence from surrounding strata. Resultant interpretations, microbial or non-microbial, should be couched within a reasonable degree of uncertainty. This approach recognizes that morphological similarity alone does not constitute scientific proof of a common origin, and reinstates a passive descriptive terminology for sedimentary surface textures that cannot be achieved with the current MISS lexicon. It is hoped that this new terminology will reduce the number of overly sensational and misleading claims of MISS occurrence, and permit the means to practically separate initial observation from interpretation. Furthermore, this methodology offers a scientific approach that appreciates the low likelihood of conclusively identifying microbial structures from visual appearance alone, informing the search for true MISS in Earth's geological record and potentially on other planetary bodies such as Mars

Application of Metapopulation Theory to Northern Bobwhite Conservation

Northern bobwhite (Colinus virginianus) populations have declined throughout the majority of the species’ range, and have experienced the largest declines in fragmented habitats, suggesting landscape scale processes may be responsible for this decline. We used the results from a stochastic population dynamics model of South Texas bobwhites as conceptual justification for use of metapopulation theory in bobwhite management. Annual quasi-extinction probabilities for isolated bobwhite populations were 0.003 (95% CI: 0.001 0.006), 0.105 (95% CI: 0.083 0.126), and 0.773 (95% CI: 0.750 0.796) for simulated populations harvested at 20, 30, and 40% annually. The probability of regional persistence at 30% harvest increased to ~ 100% in scenarios where we modeled 5 occupied hypothetical 800-ha habitat patches; however, at 40% harvest rates, probability of regional metapopulation persistence did not reach 95% until 12 habitat patches were occupied. This suggests bobwhites probably require somewhere from 800 to 9,600 ha of available habitat space to maintain 95% probability of regional metapopulation persistence as harvest varies from 0 to 40% annually. Our results have strong implications for bobwhite harvest management given the high probability of quasi-extinction of isolated populations at rates of harvest 25%. Multiple patches of habitat (where individual patch size is 800 ha) must be available to ensure bobwhite metapopulation persistence

Experimental transmission of chronic wasting disease agent from mule deer to cattle by the intracerebral route

This communication reports final observations on experimental transmission of chronic wasting disease (CWD) from mule deer to cattle by the intracerebral route. Thirteen calves were inoculated intracerebrally with brain suspension from mule deer naturally affected with CWD. Three other calves were kept as uninoculated controls. The experiment was terminated 6 years after inoculation. During that time, abnormal prion protein (PrPres) was demonstrated in the central nervous system (CNS) of 5 cattle by both immunohistochemistry and Western blot. However, microscopic lesions suggestive of spongiform encephalopathy (SE) in the brains of these PrPres-positive animals were subtle in 3 cases and absent in 2 cases. Analysis of the gene encoding bovine PRNP revealed homozygosity for alleles encoding 6 octapeptide repeats, serine (S) at codon 46, and S at codon 146 in all samples. Findings of this study show that although PrPres amplification occurred after direct inoculation into the brain, none of the affected animals had classic histopathologic lesions of SE. Furthermore, only 38% of the inoculated cattle demonstrated amplification of PrPres. Although intracerebral inoculation is an unnatural route of exposure, this experiment shows that CWD transmission in cattle could have long incubation periods (up to 5 years). This finding suggests that oral exposure of cattle to CWD agent, a more natural potential route of exposure, would require not only a much larger dose of inoculum but also may not result in amplification of PrPres within CNS tissues during the normal lifespan of cattle

Experimental transmission of chronic wasting disease agent from mule deer to cattle by the intracerebral route

This communication reports final observations on experimental transmission of chronic wasting disease (CWD) from mule deer to cattle by the intracerebral route. Thirteen calves were inoculated intracerebrally with brain suspension from mule deer naturally affected with CWD. Three other calves were kept as uninoculated controls. The experiment was terminated 6 years after inoculation. During that time, abnormal prion protein (PrPres) was demonstrated in the central nervous system (CNS) of 5 cattle by both immunohistochemistry and Western blot. However, microscopic lesions suggestive of spongiform encephalopathy (SE) in the brains of these PrPres-positive animals were subtle in 3 cases and absent in 2 cases. Analysis of the gene encoding bovine PRNP revealed homozygosity for alleles encoding 6 octapeptide repeats, serine (S) at codon 46, and S at codon 146 in all samples. Findings of this study show that although PrPres amplification occurred after direct inoculation into the brain, none of the affected animals had classic histopathologic lesions of SE. Furthermore, only 38% of the inoculated cattle demonstrated amplification of PrPres. Although intracerebral inoculation is an unnatural route of exposure, this experiment shows that CWD transmission in cattle could have long incubation periods (up to 5 years). This finding suggests that oral exposure of cattle to CWD agent, a more natural potential route of exposure, would require not only a much larger dose of inoculum but also may not result in amplification of PrPres within CNS tissues during the normal lifespan of cattle

Non linear equation of state and effective phantom divide in brane models

Here, DGP model of brane-gravity is analyzed and compared with the standard general relativity and Randall-Sundrum cases using non-linear equation of state. Phantom fluid is known to violate the weak energy condition. In this paper, it is found that this characteristic of phantom energy is affected drastically by the negative brane-tension $\lambda$ of the RS-II model. It is found that in DGP model strong energy condition(SEC) is always violated and the universe accelerates only where as in RS-II model even SEC is not violated for $1 < \rho/\lambda < 2$ and the universe decelerates

Activation of the beta interferon promoter by paramyxoviruses in the absence of virus protein synthesis

Conflicting reports exist regarding the requirement for virus replication in interferon (IFN) induction by paramyxoviruses. Our previous work has demonstrated that pathogen-associated molecular patterns capable of activating the IFN-induction cascade are not normally generated during virus replication, but are associated instead with the presence of defective interfering (DI) viruses. We demonstrate here that DIs of paramyxoviruses, including parainfluenza virus 5, mumps virus and Sendai virus, can activate the IFN-induction cascade and the IFN-β promoter in the absence of virus protein synthesis. As virus protein synthesis is an absolute requirement for paramyxovirus genome replication, our results indicate that these DI viruses do not require replication to activate the IFN-induction cascade