Segmental isotopic labeling of HIV-1 capsid protein assemblies for solid state NMR

Recent studies of noncrystalline HIV-1 capsid protein (CA) assemblies by our laboratory and by Polenova and coworkers (Protein Sci 19:716–730, 2010; J Mol Biol 426:1109–1127, 2014; J Biol Chem 291:13098–13112, 2016; J Am Chem Soc 138:8538–8546, 2016; J Am Chem Soc 138:12029–12032, 2016; J Am Chem Soc 134:6455–6466, 2012; J Am Chem Soc 132:1976–1987, 2010; J Am Chem Soc 135:17793–17803, 2013; Proc Natl Acad Sci USA 112:14617–14622, 2015; J Am Chem Soc 138:14066–14075, 2016) have established the capability of solid state nuclear magnetic resonance (NMR) measurements to provide site-specific structural and dynamical information that is not available from other types of measurements. Nonetheless, the relatively high molecular weight of HIV-1 CA leads to congestion of solid state NMR spectra of fully isotopically labeled assemblies that has been an impediment to further progress. Here we describe an efficient protocol for production of segmentally labeled HIV-1 CA samples in which either the N-terminal domain (NTD) or the C-terminal domain (CTD) is uniformly ¹⁵N,¹³C-labeled. Segmental labeling is achieved by trans-splicing, using the DnaE split intein. Comparisons of two-dimensional solid state NMR spectra of fully labeled and segmentally labeled tubular CA assemblies show substantial improvements in spectral resolution. The molecular structure of HIV-1 assemblies is not significantly perturbed by the single Ser-to-Cys substitution that we introduce between NTD and CTD segments, as required for trans-splicing.     

Theoretical study of the interaction between molecular oxygen and tetraaza macrocyclic manganese complexes

Theoretical chemistry calculations using the Density Functional Theory (DFT) were carried out to understand the interaction between oxygen (O₂) and MnN₄ type manganese-based complexes during the formation of MnN₄-O₂ adducts. In order to understand how this interaction is affected by different macrocyclic ligands, O₂ was bonded to manganese-porphyrin (MnP), manganese-octamethylporphyrin (MnOMP), manganese-tetraaza[14]annulene (MnTAA), manganese-dibenzo [b,i] [1, 4, 8, 11]-tetraaza [14] annulene (MnDBTAA), manganese-2,3,9,10-tetramethyl-1,4,8,11-tetraazacyclotetradeca-1,3,8,10-tetraene ([(tim)Mn]²⁺), and manganese-2,3,9,10-tetraphenyl-1,4,8,11-tetraazacyclotetradeca-1,3,8,10-tetraene ([(ph-tim)Mn]²⁺). The binding and activation of the oxygen molecule was facilitated by an increasing trend in the O-O bond lengths and a decreasing one in the O-O vibrational frequency, with preference for the O₂ side-on interaction among MnN₄ macrocycles. The catalytic activities of the MnN₄ complexes toward the O₂ binding process increased in the following order: [(ph-tim)Mn]²⁺?<?MnP?<?MnOMP?<?MnDBTAA?<?MnTAA?<?[(tim)Mn]²⁺. Therefore, it was concluded that the [(tim)Mn]²⁺complex was the most active for the binding and activation of molecular oxygen.     

First-principle investigation on growth patterns and properties of cobalt-doped lithium nanoclusters

A systematic theoretical investigation on cobalt lithium clusters Li_nCo [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12] was performed with a DFT approach. The location of global minima and structural evolution were carried out using the partical swarm optimization method. Li₆Co is the transition structure in going from low-coordinated structures to three-dimensional torispherical structures with a cobalt atom enclosed by lithium atoms. Maxima of ?₂ E and E _b for Li_nCo were found at n?=?3, 6, 8, 10, indicating that these clusters possess higher relative stability than their neighbors. In comparison with small clusters, n?=?1–6, the greater electron transfer from Li-2s to Co-3d within cage-like clusters Li_nCo (n?=?7–12) strengthens the bonding effect between Li_n and Co, which is reflected in the Wiberg bond index of Co and atomic binding energy analysis. AdNDP analysis verified the presence of both Lewis bonding elements (1c–2e objects) and delocalized bonding elements (6c–2e, 9c–2e and 10c–2e bonds). It is hoped that this theoretical work will provide favorable information to help understand the influence of dopant transition metal atoms on the properties of lithium-based materials.     

Use of CD40L immunoconjugates to overcome the defective immune response to vaccines for infections and cancer in the aged

Multiple investigators have reported thepresence of defects in the immune response of the elderly [Castle In: Clin Infect Dis 31:578, 2000; Ortqvist et al. In: Eur Respir J 30:414–422, 2007; Saurwein-Teissl et al. In: J Immunol 168:5893, 2002; Haynes et al. In: Proc Natl Acad Sci USA 100:15053–15058, 2003]. These defects reduce the magnitude of the immune response to infection and to vaccination. In individuals greater than 55 years of age, the probability of developing a fully protective neutralizing antibody response to the yearly multivalent particle inactivated influenza vaccine is less than 20% [Jefferson et al. In: Lancet 264:1165–1174, 2005; Goodwin et al. In: Vaccine 24:1159–1169, 2006; Jackson et al. In: Lancet 372:398–405, 2008; Simonsen and Taylor In: Lancet 7:658–666, 2007]. The defects in the aged immune system that are responsible for this limited response to vaccination in the older age groups include functional defects of the antigen presenting cells, functional defects in CD4 helper CD4 T cells and monocytes, and an altered microenvironment [Eaton et al. In: J Exp Med 200:1613–1622, 2004; Dong et al. In: J Gen Virol 84:1623–1628, 2003; Deng et al. In: Immunology 172:3437–3446, 2004; Cella et al. In: J Exp Med 184:747–752, 1996]. Starting at puberty, the involution of the thymus and the consequent reduction of the export of naïve T cells specific to neo-antigens leads to the reduction of the ratio of antigen naïve to memory cells as chronological age advances [Prelog In: AutoimmunRev 5:136–139, 2006; McElhaney et al. In: J Immunology 176:6333–6339, 2006]. Changes in glycosylation of T cells and target antigens acquired during the aging process and the antibodies to these new glycopeptides and glycoproteins may also contribute to a reduction in the functioning of the adaptive immune response [Ishii et al. In: J Clin Neurosci 14:110–115, 2007; Shirai et al. In: Clin Exp Immunol 12:455–464, 1972; Adkins and Riley In: Mech AgeingDev 103:147–164, 1998; Ben-Yehuda and Weksler In: Cancer Investigation 10:525–531, 1992]. One of the more interesting examples of the functional defects in the cells of the adaptive immune response is a reduced level of expression in the surface cytoadhesion and activation receptor molecules on CD4 helper T cells undergoing activation during vaccination. Upon infection or vaccination, CD40L is typically increased on the surface of CD4 helper T cells during activation, and this increased expression is absolutely essential to the CD40L promotion of expansion of antigen-specific B cells and CD 8 effector T cells in response to infection or vaccination [Singh et al. In: Protein Sci 7:1124–1135, 1998; Grewal and Flavell In: Immunol Res 16: 59–70, 1997; Kornbluth In: J Hematother Stem Cell Res 11:787–801, 2002; Garcia de Vinuesa et al. In: Eur J Immunol 29:3216–3224, 1999]. In aged human beings and mice, the reduced levels of expression of CD40 ligand (CD40L) in activated CD4 helper T cells is dramatically reduced [Eaton et al. In: J Exp Med 200:1613–1622, 2004; Dong et al. In: J Gen Virol 84:1623–1628, 2003]. To circumvent the reduction in CD40L expression and the subsequent reduction in immune response in the elderly, we have developed a chimeric vaccine comprised of the CD40L linked to the target antigen, in a replication incompetent adenoviral vector and in booster protein. This review will discuss the implementation the potential use of this approach for the vaccination of the older populations for cancer and infection.     

Metabolite targeting: development of a comprehensive targeted metabolomics platform for the assessment of diabetes and its complications

Biomarker studies for metabolic disorders like diabetes mellitus (DM) are an important approach towards a better understanding of the underlying pathophysiological mechanisms of diseases (Roberts and Gerszten in Cell Metab 18:43–50, 2013; Wilson et al. in Proteome Res 4:591–598, 2005). Furthermore, screening of potential metabolic biomarkers opens the opportunity of early diagnosis as well as therapy and drug monitoring of metabolic disorders (Rhee et al. in J Clin Invest 10:1–10, 2011; Wang et al. in Nat Med 17:448–458, 2011; Wenk in Nat Rev Drug Discov 4:594–610, 2005). The aim of the present study was to develop methods for the quantitative determination of 74 potential metabolite biomarkers for DM and diabetic nephropathy (DN) in serum. Several studies have shown that the concentrations of many polar metabolites like amino or organic acids are changed in subjects suffering from diabetes (Wang et al. in Nat Med 17:448–458, 2011; Yuan et al. in J Chromatogr B 813:53–58, 2007). Analyzing polar analytes presents a challenge in liquid chromatography (LC) coupled with ESI–MS/MS (Gika et al. in J Sep Sci 31:1598–1608, 2008; Spagou et al. in J Sep Sci 33:716–727, 2010). Considering those reasons we decided to develop a specific HILIC–ESI–QqQ–MS/MS-method for quantitative determination of these polar metabolites. A subsequent method validation was carried out for both HILIC and RP chromatography with respect to the guidelines of the Food and Drug Administration (FDA in Food and Drug Administration: Guidance for industry, bioanalytical method validation, 2001). The HILIC and RP LC–MS methods were successfully validated. Furthermore, the HILIC method presented here was applied to serum samples of GIPR^dn transgenic mice, a diabetic strain developing DN, and non transgenic littermate controls. Significant, diabetes-associated changes were observed for the concentrations of 21 out of 62 metabolites. The new methods described here accurately quantify 74 metabolites known to be regulated in diabetes, allowing for direct comparison between studies and laboratories. Thus, these methods may be highly adoptable in clinical research, providing a starting point for early diagnosis and metabolic screening.     

Weak radicals,weak suppletion,and phonological indices in Semitic

Paster (2014) has argued that grammar does not distinguish between weak and strong suppletion. This claim is countered in this paper, in an analysis of allomorphic effects in several Semitic languages. What has been traditionally called “root” is broken down into three levels: the formless index (Harley 2014), the phonological index (Borer 2005, 2009, 2013) and its underlying representation. The distinction between the first two leads to a principled structural difference between weak and strong suppletion. Several test cases are presented that require a distinction between the latter two. Two general conclusions are drawn: (1) allomorphy at the different levels has different functions, and (2) in the Semitic root-and-pattern system, weakly suppletive allomorphy never targets the root as a whole; there is no root allomorphy in Semitic.     

Plant individuality: a solution to the demographer’s dilemma

The problem of plant individuality is something which has vexed botanists throughout the ages, with fashion swinging back and forth from treating plants as communities of individuals (Darwin 1800; Braun and Stone 1853; Münch 1938) to treating them as organisms in their own right, and although the latter view has dominated mainstream thought most recently (Harper 1977; Cook 1985; Ariew and Lewontin 2004), a lively debate conducted mostly in Scandinavian journals proves that the issues are far from being resolved (Tuomi and Vuorisalo 1989b; Fagerström 1992; Pan and Price 2001). In this paper I settle the matter once and for all, by showing which elements of each side are correct.     

<Superscript>15</Superscript>N, <Superscript>13</Superscript>C and <Superscript>1</Superscript>H backbone resonance assignments of an artificially engineered TEM-1/PSE-4 class A β-lactamase chimera and its deconvoluted mutant

The widespread use of β-lactam antibiotics has given rise to a dramatic increase in clinically-relevant β-lactamases. Understanding the structure/function relation in these variants is essential to better address the ever-growing incidence of antibiotic resistance. We previously reported the backbone resonance assignments of a chimeric protein constituted of segments of the class A β-lactamases TEM-1 and PSE-4 (Morin et al. in Biomol NMR Assign 4:127–130, 2010. doi: 10.1007/s12104-010-9227-8). That chimera, cTEM17m, held 17 amino acid substitutions relative to TEM-1 β-lactamase, resulting in a well-folded and fully functional protein with increased dynamics. Here we report the ¹H, ¹³C and ¹⁵N backbone resonance assignments of chimera cTEM-19m, which includes 19 substitutions and exhibits increased active-site perturbation, as well as one of its deconvoluted variants, as the first step in the analysis of their dynamic behaviours.     

The chalicothere <Emphasis Type="Italic">Metaschizotherium bavaricum</Emphasis> (Perissodactyla,Chalicotheriidae, Schizotheriinae) from the Miocene (MN5) Lagerstätte of Sandelzhausen (Germany): description,comparison, and paleoecological significance

Within the fossil collection from the Sandelzhausen Lagerstätte in the Upper Freshwater Molasse near Mainburg, Germany, are remains of the schizotheriine chalicothere Metaschizotherium bavaricum, von Koenigswald, 1932. This new material includes elements from a large part of the body, and allows the dentition and postcranial skeleton of Metaschizotherium to be described in detail for the first time. At approximately 16 Ma (MN5), M. bavaricum is now the best-known Early and Middle Miocene European schizotheriine and is important for comparative studies. It differs to some degree from earlier Miocene (MN2–MN4) European material attributed to Moropus sp. or Metaschizotherium wetzleri (Kowalewsky, 1873) and to a larger degree from the Late Miocene species Ancylotherium pentelicum (Gaudry and Lartet, 1856). At Sandelzhausen, M. bavaricum apparently lived in a moist forested environment, where it probably fed on leaves, fruit, and seeds. Members of the Chalicotheriinae, such as Anisodon and Chalicotherium, are not found at Sandelzhausen and may not have been present in Europe at this time. M. bavaricum, like other Schizotheriinae, did not have the bizarre gorilla-like proportions of the Chalicotheriinae. Instead, its general body proportions resemble those of contemporary schizotheriine chalicotheres on other continents, for example, Moropus from North America. M. bavaricum is slightly smaller than the type species of Metaschizotherium, M. fraasi von Koenigswald, 1932 (MN6–MN7) and differs from it in small ways that are still being explored as variation within and differences between these species are clarified. The schizotheriine chalicothere from La Grive St.-Alban (France) referred to M. fraasi by von Koenigswald (Palaeontographica, Beitrage zur Naturgeschichte der Vorzeit 8:1–24, 1932) and Viret (Nouvelles Archives Musée d’Histoire Naturelle de Lyon 6:53–81, 1961) should be restudied and referred to a different taxon.     

Lexical splits within periphrasis: mixed perfective auxiliation systems in Italo-Romance

This paper addresses the phenomenon of mixed paradigms, i.e. mixed perfective auxiliation systems, attested in a wide range of Italo-Romance varieties (cf. Loporcaro 2001, 2007a, 2014; Manzini and Savoia 2005, among others). In these varieties, two auxiliary verbs, esse and habere, alternate within one and the same (sub)paradigm, displaying various patterns which can range from morphosyntactically motivated to apparently unmotivated distributions (here termed ‘morphomic’). I propose that, in these varieties, auxiliary selection is no longer a syntactically driven phenomenon, but becomes morphologized. I draw on the notion of ‘lexical split’ (cf. Corbett 2013, 2015, 2016) and describe the attested splits induced by intraparadigmatic auxiliary alternation. Following Bonami (2015), I put forward a typology of such splits. It is shown that, apart from motivated distributions, some morphomic patterns can also be found. The typology becomes more complex insofar as patterns with free variation between both auxiliaries are taken into account, as well as patently morphomic patterns which also seem to display external syntactic relevance (cf. Corbett 2013: 174–176). The phenomena reviewed and discussed in this paper are of major interest because they demonstrate the existence of competing exponence strategies within periphrasis, thus enriching the notion of ‘possible lexeme’ (cf. Corbett 2015: 146).     

From possessive suffix to affective demonstrative suffix in Hungarian: a grammaticalization analysis

The non-possessive uses of possessive morphology in Uralic languages have been a topic of intense debate (Fraurud 2001; Nikolaeva 2003; Gerland 2014; Janda 2015; É. Kiss and Tánczos to appear). In this paper, I focus on a special use of the poss.3sg suffix in Hungarian constructions such as a hülyéje (the stupid-poss.3sg): lit. ‘its stupid’, meaning ‘that total idiot’. My main claim is that this suffix is an affective demonstrative suffix (Lakoff 1974; Liberman 2008; Potts and Schwarz 2010), and that it has developed as a result of grammaticalization from a full-fledged possessive construction of the form a világ hülyéje (the world stupid-poss.3sg): lit. ‘the world’s stupid’, meaning: ‘the biggest idiot in the world’. I will show that this gradual process can be reconstructed fairly accurately using historical and contemporary corpora. I also claim that this grammaticalization pathway is very natural as it is based on a set-element relationship which is often expressed by possessive constructions cross-linguistically. I also identify two parameters which facilitate this grammaticalization process: the availability of (silent) pro possessors and the lack of gender agreement on the possessive suffix. Since Uralic languages in general have these parameters, I will argue that this grammaticalization pathway should at least be considered as one of the possible sources of the demonstrative (and definiteness marking) uses of poss.3sg suffixes in Uralic languages. Finally, my results are also an important contribution to the debate on whether demonstratives can be derived from other functional elements through grammaticalization (Plank 1979; Traugott 1982; Himmelmann 1997).     

What is behind “centromere repositioning”?

An increasing number of observations suggest an evolutionary switch of centromere position on monocentric eukaryotic chromosomes which otherwise display a conserved sequence of genes and markers. Such observations are particularly frequent for primates and equidae (for review see Heredity 108:59–67, 2012) but occur also in marsupials (J Hered 96:217–224, 2005) and in plants (Chromosome Res 25:299–311, 2017 and references therein). The actual mechanism(s) behind remained unclear in many cases (Proc Natl Acad Sci USA 101:6542–6547, 2004; Trends Genet 30:66–74, 2014). The same is true for de novo centromere formation on chromosomes lacking an active centromere. This article focuses on recent reports on centromere repositioning and possible mechanisms behind and addresses open questions.     

Strong Comma-Free Codes in Genetic Information

Comma-free codes constitute a class of circular codes, which has been widely studied, in particular by Golomb et al. (Biologiske Meddelelser, Kongelige Danske Videnskabernes Selskab 23:1–34, 1958a, Can J Math 10:202–209, 1958b), Michel et al. (Comput Math Appl 55:989–996, 2008a, Theor Comput Sci 401:17–26, 2008b, Inf Comput 212:55–63, 2012), Michel and Pirillo (Int J Comb 2011:659567, 2011), and Fimmel and Strüngmann (J Theor Biol 389:206–213, 2016). Based on a recent approach using graph theory to study circular codes Fimmel et al. (Philos Trans R Soc 374:20150058, 2016), a new class of circular codes, called strong comma-free codes, is identified. These codes detect a frameshift during the translation process immediately after a reading window of at most two nucleotides. We describe several combinatorial properties of strong comma-free codes: enumeration, maximality, self-complementarity and \(CF^3\)-property (comma-free property in all the three possible frames). These combinatorial results also highlight some new properties of the genetic code and its evolution. Each amino acid in the standard genetic code is coded by at least one strong comma-free code of size 1. There are 9 amino acids \(S=\{Asn,Asp,Gln,Gly,Lys,Met,Phe,Pro,Trp\}\) among 20 such that for each amino acid from S, its synonymous trinucleotide set (excluding the necessary periodic trinucleotides \(\{AAA,CCC,GGG,TTT\}\)) is a strong comma-free code. The primeval comma-free RNY code of Eigen and Schuster (Naturwissenschaften 65:341–369, 1978) is a self-complementary \(CF^3\)-code of size 16. Furthermore, it is the union of two strong comma-free codes of size 8 which are complementary to each other.     

Production of Estonian case-inflected nouns shows whole-word frequency and paradigmatic effects

Most psycholinguistic models of lexical processing assume that the comprehension and production of inflected forms is mediated by morphemic constituents. Several more recent studies, however, have challenged this assumption by providing empirical evidence that information about individual inflected forms and their paradigmatic relations is available in long-term memory (Baayen et al. 1997; Milin et al. 2009a, 2009b). Here, we investigate how whole-word frequency, inflectional paradigm size and morphological family size affect production latencies and articulation durations when subjects are asked to read aloud isolated Estonian case-inflected nouns. In Experiment 1, we observed that words with a larger morphological family elicited shorter speech onset latencies, and that forms with higher whole-word frequency had shorter acoustic durations. Experiment 2, for which we increased statistical power by using 2,800 words, revealed that higher whole-word frequency, inflectional paradigm size, and morphological family size reduced both speech onset times and acoustic durations. These results extend our knowledge of morphological processing in three ways. First, whole-word frequency effects of inflected forms in morphologically rich languages are not restricted to a small number of very high-frequency forms, contrary to previous claims (Niemi et al. 1994; Hankamer 1989; Yang 2016). Second, we replicated the morphological family size effect in a new domain, the acoustic durations of inflected forms. Third, we showed that a novel paradigmatic measure, inflectional paradigm size, predicts word naming latencies and acoustic durations. These results fit well with Word-and-Paradigm morphology (Blevins 2016) and argue against strictly (de)compositional models of lexical processing.     

Mathematical Model of Bone Remodeling Captures the Antiresorptive and Anabolic Actions of Various Therapies

A better understanding of the molecular pathways regulating the bone remodeling process should help in the development of new antiresorptive regulators and anabolic regulators, that is, regulators of bone resorption and of bone formation. Understanding the mechanisms by which parathyroid hormone (PTH) influences bone formation and how it switches from anabolic to catabolic action is important for treating osteoporosis (Poole and Reeve in Curr Opin Pharmacol 5:612–617, 2005). In this paper we describe a mathematical model of bone remodeling that incorporates, extends, and integrates several models of particular aspects of this biochemical system (Cabal et al. in J Bone Miner Res 28(8):1830–1836, 2013; Lemaire et al. in J Theor Biol 229:293–309, 2004; Peterson and Riggs in Bone 46:49–63, 2010; Raposo et al. in J Clin Endocrinol Metab 87(9):4330–4340, 2002; Ross et al. in J Disc Cont Dyn Sys Series B 17(6):2185–2200, 2012). We plan to use this model as a bone homeostasis platform to develop anabolic and antiresorptive compounds. The model will allow us to test hypotheses about the dynamics of compounds and to test the potential benefits of combination therapies. At the core of the model is the idealized account of osteoclast and osteoblast signaling given by Lemaire et al. (J Theor Biol 229:293–309, 2004). We have relaxed some of their assumptions about the roles of osteoprotegerin, transforming growth factor \(\upbeta \), and receptor activator of nuclear factor \(\upkappa \)B ligand; we have devised more detailed models of the interactions of these species. We have incorporated a model of the effect of calcium sensing receptor antagonists on remodeling (Cabal et al. in J Bone Miner Res 28(8):1830–1836, 2013). We have also incorporated a basic model of the effects of vitamin D on calcium homeostasis. We have included a simple model of the mechanism proposed by Bellido et al. (2003), Ross et al. (J Disc Cont Dyn Sys Series B 17(6):2185–2200, 2012), of the influence of PTH on osteoblast apoptosis, a mechanism that accounts for the anabolic response to pulsatile PTH administration. Finally, we have devised a simple model of the administration and effects of bisphosphonates. The biomarkers in the model are procollagen type 1 amino-terminal propeptide and C-terminal telopeptide. Bone mineral density is the model’s principal endpoint.     

Using the product environmental footprint for supply chain management: lessons learned from a case study on pork

Purpose

The purpose of this study was to test the chain-organization environmental footprint (chain-OEF) approach by applying it to part of a pork production chain in Belgium. The approach is supposed to provide insight into the environmental impact of a specific production chain in an efficient manner by applying pragmatic data collection throughout the chain. This is achieved by allocating the environmental impact of each of the production sites to the product of interest using straightforward allocation rules.

Methods

The cradle-to-gate (up to retail) environmental impact of pork was determined by life cycle assessment (LCA), in line with the product and organisation environmental footprint guidelines (PEF and OEF; European Commission 2013b). Foreground data was gathered at a feed production site, two farmers, a slaughterhouse and a meat processing site. All foreground operations are part of the same pork production chain in Belgium. The chain was completed using background data from Ecoinvent v3.01 (Wernet et al. 2016), Agri-Footprint v1.0 (Blonk 2014), European Life Cycle Database v3.0, LCA Food Database (Nielsen et al. 2003) and OEF Sector Rules Retail (Humbert et al. 2015b). The impact was quantified using the international reference life cycle data system (ILCD) midpoint method for 14 impact categories, but focussing on climate change.

Results and discussion

The total carbon footprint of the cradle-to-gate pork production system equals 0.46 kg CO₂-eq. (100 g pork)^?1. This result is quite similar to that of earlier studies analysing the pork production chain: 0.58 and 0.57 kg CO₂-eq. (100 g pork)^?1 (Bracquené et al. 2011, Agri-Footprint 2014). Most of the carbon footprint was caused by feed production and more specifically, by the feed ingredients and their transport. Grains, soy and palm oil have the largest impact contributions. The farms are responsible for most of the remaining impact. N₂O and CH₄ emissions are the largest cause of greenhouse gas emissions at the farms. Also, in the other 13 considered impact categories, feed production and farming are responsible for more than half of the total impact, mostly followed by meat processing.

Conclusions

Applying the chain-OEF approach in this study has shown that a chain LCA can be performed successfully and pragmatic data collection allows obtaining LCA results relatively fast, especially for small or medium-sized enterprises (SMEs). Whereas data availability was not such an issue, the main bottlenecks identified are data management and the link of LCA to other disciplines such as engineering, policy, etc. which could increase the added value of LCA studies.

     

Spinicaudata (“Conchostraca,” Crustacea) from the Middle Keuper (Upper Triassic) of the southern Germanic Basin,with a review of Carnian–Norian taxa and suggested biozones

The Coburg Sandstone member of the Hassberge Formation, Middle Keuper, Carnian, Upper Triassic, in the Germanic Basin of Central Europe contains spinicaudatan branchiopods which considerably broaden the known spectrum and provide important data on the phylogenetic history and intercontinental correlation of this systematic group. The spinicaudatan fauna for this lithostratigraphic unit is described in detail and includes Euestheria kozuri sp. nov., E.? sp. nov. A, Gregoriusella striatula sp. nov., Laxitextella freybergi Kelber and Kozur in Kozur and Weems, 2007, L. dorsorecta (Reible, 1962), and Laxitextella? sp. A. Additional discussions deal with Euestheria multicostata (Geyer, 1987), E. winterpockensis (Bock, 1953a), Laxitextella laxitexta (Sandberger in Jones, 1890), Laxitextella multireticulata (Reible, 1962), and “Laxitextella? hausmanni (Schmidt, 1938),” as well as problems with (sub)global zonations that are based on spinicaudatans and suggested to be of Carnian and Norian age.     

Chemical Analysis of a “Miller-Type” Complex Prebiotic Broth

In a famous experiment Stanley Miller showed that a large number of organic substances can emerge from sparking a mixture of methane, ammonia and hydrogen in the presence of water (Miller, Science 117:528–529, 1953). Among these substances Miller identified different amino acids, and he concluded that prebiotic events may well have produced many of Life’s molecular building blocks. There have been many variants of the original experiment since, including different gas mixtures (Miller, J Am Chem Soc 77:2351–2361, 1955; Oró Nature 197:862–867, 1963; Schlesinger and Miller, J Mol Evol 19:376–382, 1983; Miyakawa et al., Proc Natl Acad Sci 99:14,628–14,631, 2002). Recently some of Miller’s remaining original samples were analyzed with modern equipment (Johnson et al. Science 322:404–404, 2008; Parker et al. Proc Natl Acad Sci 108:5526–5531, 2011) and a total of 23 racemic amino acids were identified. To give an overview of the chemical variety of a possible prebiotic broth, here we analyze a “Miller type” experiment using state of the art mass spectrometry and NMR spectroscopy. We identify substances of a wide range of saturation, which can be hydrophilic, hydrophobic or amphiphilic in nature. Often the molecules contain heteroatoms, with amines and amides being prominent classes of molecule. In some samples we detect ethylene glycol based polymers. Their formation in water requires the presence of a catalyst. Contrary to expectations, we cannot identify any preferred reaction product. The capacity to spontaneously produce this extremely high degree of molecular variety in a very simple experiment is a remarkable feature of organic chemistry and possibly prerequisite for Life to emerge. It remains a future task to uncover how dedicated, organized chemical reaction pathways may have arisen from this degree of complexity.     

Metastasis as supra-cellular selection? A reply to Lean and Plutynski

In response to Germain (Biol Philos 27:785–810, 2012. doi: 10.1007/s10539-012-9334-2) argument that evolution by natural selection has a limited explanatory power in cancer, Lean and Plutynski (Biol Philos 31:39–57, 2016. doi: 10.1007/s10539-015-9511-1) have recently argued that many adaptations in cancer only make sense at the tumor level, and that cancer progression mirrors the major evolutionary transitions. While we agree that selection could potentially act at various levels of organization in cancers, we argue that tumor-level selection (MLS2) is unlikely to actually play a relevant role in our understanding of the somatic evolution of human cancers.