Microevolution of Anthrax from a Young Ancestor (M.A.Y.A.) Suggests a Soil-Borne Life Cycle of Bacillus anthracis

During an anthrax outbreak at the Pollino National Park (Basilicata, Italy) in 2004, diseased cattle were buried and from these anthrax-foci Bacillus anthracis endospores still diffuse to the surface resulting in local accumulations. Recent data suggest that B. anthracis multiplies in soil outside the animal-host body. This notion is supported by the frequent isolation of B. anthracis from soil lacking one or both virulence plasmids. Such strains represent an evolutionary dead end, as they are likely no longer able to successfully infect new hosts. This loss of virulence plasmids is explained most simply by postulating a soil-borne life cycle of the pathogen. To test this hypothesis we investigated possible microevolution at two natural anthrax foci from the 2004 outbreak. If valid, then genotypes of strains isolated from near the surface at these foci should be on a different evolutionary trajectory from those below residing in deeper-laying horizons close to the carcass. Thus, the genetic diversity of B. anthracis isolates was compared conducting Progressive Hierarchical Resolving Assays using Nucleic Acids (PHRANA) and next generation Whole Genome Sequencing (WGS). PHRANA was not discriminatory enough to resolve the fine genetic relationships between the isolates. Conversely, WGS of nine isolates from near-surface and nine from near-carcass revealed five isolate specific SNPs, four of which were found only in different near-surface isolates. In support of our hypothesis, one surface-isolate lacked plasmid pXO1 and also harbored one of the unique SNPs. Taken together, our results suggest a limited soil-borne life cycle of B. anthracis.     

Rewriting the Central European Early Bronze Age Chronology: Evidence from Large-Scale Radiocarbon Dating

The transition from the Neolithic to the Early Bronze Age in Central Europe has often been considered as a supra-regional uniform process, which led to the growing mastery of the new bronze technology. Since the 1920s, archaeologists have divided the Early Bronze Age into two chronological phases (Bronze A1 and A2), which were also seen as stages of technical progress. On the basis of the early radiocarbon dates from the cemetery of Singen, southern Germany, the beginning of the Early Bronze Age in Central Europe was originally dated around 2300/2200 BC and the transition to more complex casting techniques (i.e., Bronze A2) around 2000 BC. On the basis of 140 newly radiocarbon dated human remains from Final Neolithic, Early and Middle Bronze Age cemeteries south of Augsburg (Bavaria) and a re-dating of ten graves from the cemetery of Singen, we propose a significantly different dating range, which forces us to re-think the traditional relative and absolute chronologies as well as the narrative of technical development. We are now able to date the beginning of the Early Bronze Age to around 2150 BC and its end to around 1700 BC. Moreover, there is no transition between Bronze (Bz) A1 and Bronze (Bz) A2, but a complete overlap between the type objects of the two phases from 1900–1700 BC. We thus present a revised chronology of the assumed diagnostic type objects of the Early Bronze Age and recommend a radiocarbon-based view on the development of the material culture. Finally, we propose that the traditional phases Bz A1 and Bz A2 do not represent a chronological sequence, but regionally different social phenomena connected to the willingness of local actors to appropriate the new bronze technology.     

Organic Tracers from Asphalt in Propolis Produced by Urban Honey Bees,Apis mellifera Linn.

Propolis is a gummy material produced by honey bees to protect their hives and currently has drawn the attention of researchers due to its broad clinical use. It has been reported, based only on observations, that honey bees also collect other non-vegetation substances such as paint or asphalt/tar to make propolis. Therefore, propolis samples were collected from bee hives in Riyadh and Al-Bahah, a natural area, Saudi Arabia to determine their compositional characteristics and possible sources of the neutral organic compounds. The samples were extracted with hexane and analyzed by gas chromatography-mass spectrometry. The results showed that the major compounds were n-alkanes, n-alkenes, methyl n-alkanoates, long chain wax esters, triterpenoids and hopanes. The n-alkanes (ranging from C₁₇ to C₄₀) were significant with relative concentrations varying from 23.8 to 56.8% (mean = 44.9+9.4%) of the total extracts. Their odd carbon preference index (CPI) ranged from 3.6 to 7.7, with a maximum concentration at heptacosane indicating inputs from higher plant vegetation wax. The relative concentrations of the n-alkenes varied from 23.8 to 41.19% (mean = 35.6+5.1%), with CPI = 12.4-31.4, range from C₂₅ to C₃₅ and maximum at tritriacontane. Methyl n-alkanoates, ranged from C₁₂ to C₂₆ as acids, with concentrations from 3.11 to 33.2% (mean = 9.6+9.5%). Long chain wax esters and triterpenoids were minor. The main triterpenoids were α- and β-amyrins, amyrones and amyryl acetates. The presence of hopanes in some total extracts (up to 12.5%) indicated that the bees also collected petroleum derivatives from vicinal asphalt and used that as an additional ingredient to make propolis. Therefore, caution should be taken when considering the chemical compositions of propolis as potential sources of natural products for biological and pharmacological applications. Moreover, beekeepers should be aware of the proper source of propolis in the flight range of their bee colonies.     

Mechanistic study of CMP-Neu5Ac hydrolysis by α2,3-sialyltransferase from Pasteurella dagmatis

Bacterial sialyltransferases of the glycosyltransferase family GT-80 exhibit pronounced hydrolase activity toward CMP-activated sialyl donor substrates. Using in situ proton NMR, we show that hydrolysis of CMP-Neu5Ac by Pasteurella dagmatis α2,3-sialyltransferase (PdST) occurs with axial-to-equatorial inversion of the configuration at the anomeric center to release the α-Neu5Ac product. We propose a catalytic reaction through a single displacement-like mechanism where water replaces the sugar substrate as a sialyl group acceptor. PdST variants having His²⁸⁴ in the active site replaced by Asn, Asp or Tyr showed up to 10⁴-fold reduced activity, but catalyzed CMP-Neu5Ac hydrolysis with analogous inverting stereochemistry. The proposed catalytic role of His²⁸⁴ in the PdST hydrolase mechanism is to facilitate the departure of the CMP leaving group.     

Sea-level changes as controlling factor of early diagenesis: the reefal limestones of Adnet (Late Triassic,Northern Calcareous Alps,Austria)

The uppermost Rhaetian Adnet reef is part of the Dachstein carbonate platform and is situated at the transition to the intrashelf Kössen Basin. Its diagenetic evolution is investigated focusing on dissolution cavities in the Tropfbruch quarry of Adnet (near Salzburg) stratigraphically situated immediately below the Triassic–Jurassic boundary. Sea-level changes due to global eustatic trends and regional tectonics are assumed to be the controlling factors in the development of a manifold diagenetic sequence characterized by phases of meteoric dissolution, marine and burial cementation, and internal sedimentation. Despite small-scale variations of the sequence, a superordinate pattern of diagenetic phases could be elaborated. Small-scale eustatic sea-level falls subordinate to a global regression trend caused subaerial exposures of the Adnet reef in the latest Rhaetian to earliest Hettangian. The result was karstification and meteoric dissolution of aragonitic coral skeletons (Retiophyllia) leading to the formation of biomoldic porosity. Coral septa which escaped dissolution were transformed into neomorphic calcite spar under meteoric–phreatic conditions. A first generation of dog-tooth cements precipitated sporadically on the altered coral skeletons. Eustatic sea-level rise in Early to Mid-Hettangian times caused a renewed flooding of the pore space of the Adnet reef by marine water and the influx of a first generation of internal sediments (IS I), derived from the karstified host rock of the Upper Rhaetian reef limestone. These internal sediments are overgrown by radiaxial-fibrous calcites (RFCs) whose oxygen-isotopic signature (δ¹⁸O = ?1.3 (±0.7)‰) indicates precipitation in deeper (colder) water (18–21°C) due to a first phase of drowning. An intermediate phase of eustatic sea-level lowstand in the Late Hettangian is expressed by dissolution and corrosion of RFCs. Rapid drowning of the Dachstein carbonate platform due to eustatic sea-level rise and tectonic movements took place in the Early Sinemurian and a second generation of internal sediments (IS II) derived from the Lower Sinemurian Adnet Formation is washed into the dissolution cavities. Where IS II is absent, RFCs are overgrown by a second generation of dog-tooth cements with a bright-luminescent outer rim indicating the transition to negative redox conditions in the pore water during shallow burial. Burial diagenesis is represented by blocky calcite cements which occlude the remaining pore space. Depleted oxygen-isotope values and significant Fe contents indicate precipitation under reducing redox conditions and elevated temperatures of 30–50°C at burial depths of 420–870 m. Locally, replacive saddle dolomite is the latest diagenetic phase in the Adnet reef indicating crystallization under hydrothermal influences related to compressional subduction regimes of the Penninic Ocean.     

SIRT2-mediated protein deacetylation: An emerging key regulator in brain physiology and pathology

Protein function is considerably altered by posttranslational modification. In recent years, cycles of acetylation/deacetylation emerged as fundamental regulators adjusting biological activity of many proteins. Particularly, protein deacetylation by Sirtuins, a family of atypical histone deacetylases (HDACs), was demonstrated to regulate fundamental cell biological processes including gene expression, genome stability, mitosis, nutrient metabolism, aging, mitochondrial function and cell motility. Given this wealth of biological functions, perhaps not unexpectedly then, pharmacological compounds targeting Sirtuin activity are now prime therapeutic agents for alleviating severity of major diseases encompassing diabetes, cancer, cardiovascular and neurodegenerative disorders in many organs. In this review, we will focus on the brain and its physiological and pathological processes governed by Sirtuin-mediated deacetylation. Besides discussing Sirtuin function in neurodegenerative diseases, emphasis will be given on the mounting evidence deciphering key developmental brain functions for Sirtuins in neuronal motility, neuroprotection and oligodendrocyte differentiation. In this respect, we will particularly highlight functions of the unconventional family member SIRT2 in post-mitotic neurons and glial cells.     

On-line infrared spectroscopy for bioprocess monitoring

One of the major aims of bioprocess engineering is the real-time monitoring of important process variables. This is the basis of precise process control and is essential for high productivity as well as the exact documentation of the overall production process. Infrared spectroscopy is a powerful analytical technique to analyze a wide variety of organic compounds. Thus, infrared sensors are ideal instruments for bioprocess monitoring. The sensors are non-invasive, have no time delay due to sensor response times, and have no influence on the bioprocess itself. No sampling is necessary, and several components can be analyzed simultaneously. In general, the direct monitoring of substrates, products, metabolites, as well as the biomass itself is possible. In this review article, insights are provided into the different applications of infrared spectroscopy for bioprocess monitoring and the complex data interpretation. Different analytical techniques are presented as well as example applications in different areas.     

Peptidylarginine deiminase gene is differentially expressed in freshwater and brackish water rainbow trout

Peptidylarginine deiminase (PADI)-like cDNA sequence was isolated from rainbow trout (Oncorhynchus mykiss). It consists of a 111-bp 5′-untranslated region, a 731-bp 3′-UTR, and a 2,010-bp open reading frame encoding a protein of 669 amino acids. In the presence of calcium ions, PADI enzymes catalyze the post-translational modification reaction generating citrulline residues. Mammalian PADI enzymes are involved in a number of regulatory processes during cell differentiation and development such as skin keratinization, myelin maturation, and histone deimination. Though five PADI isotypes have been isolated from mammals, in bony fish only one PADI enzyme is present, which contains conserved amino acid residues responsible for catalysis and calcium ion-binding. Sequence identity of piscine PADI protein sequences available at gene databases exceeds 67%. Phylogenetic analyses revealed that not only piscine, but also amphibian and avian PADI-like proteins share most identical amino acid residues with mammalian PADI2. mRNA level of trout PADI-like gene is high in skin, fin, gills, brain, and spleen of rainbow trout. Quantitative Real-Time RT-PCR revealed that PADI gene is differentially expressed in liver, trunk kidney, and spleen of two trout strains, the freshwater-cultured STEELHEAD trout and the brackish water strain BORN.     

Development and organization of polarity-specific segregation of primary vestibular afferent fibers in mice

A striking feature of vestibular hair cells is the polarized arrangement of their stereocilia as the basis for their directional sensitivity. In mammals, each of the vestibular end organs is characterized by a distinct distribution of these polarized cells. We utilized the technique of post-fixation transganglionic neuronal tracing with fluorescent lipid soluble dyes in embryonic and postnatal mice to investigate whether these polarity characteristics correlate with the pattern of connections between the endorgans and their central targets; the vestibular nuclei and cerebellum. We found that the cerebellar and brainstem projections develop independently from each other and have a non-overlapping distribution of neurons and afferents from E11.5 on. In addition, we show that the vestibular fibers projecting to the cerebellum originate preferentially from the lateral half of the utricular macula and the medial half of the saccular macula. In contrast, the brainstem vestibular afferents originate primarily from the medial half of the utricular macula and the lateral half of the saccular macula. This indicates that the line of hair cell polarity reversal within the striola region segregates almost mutually exclusive central projections. A possible interpretation of this feature is that this macular organization provides an inhibitory side-loop through the cerebellum to produce synergistic tuning effects in the vestibular nuclei. The canal cristae project to the brainstem vestibular nuclei and cerebellum, but the projection to the vestibulocerebellum originates preferentially from the superior half of each of the cristae. The reason for this pattern is not clear, but it may compensate for unequal activation of crista hair cells or may be an evolutionary atavism reflecting a different polarity organization in ancestral vertebrate ears.     

CK2 phosphorylation-dependent interaction between aprataxin and MDC1 in the DNA damage response

Aprataxin, defective in the neurodegenerative disorder ataxia oculomotor apraxia type 1, resolves abortive DNA ligation intermediates during DNA repair. Here, we demonstrate that aprataxin localizes at sites of DNA damage induced by high LET radiation and binds to mediator of DNA-damage checkpoint protein 1 (MDC1/NFBD1) through a phosphorylation-dependent interaction. This interaction is mediated via the aprataxin FHA domain and multiple casein kinase 2 di-phosphorylated S-D-T-D motifs in MDC1. X-ray structural and mutagenic analysis of aprataxin FHA domain, combined with modelling of the pSDpTD peptide interaction suggest an unusual FHA binding mechanism mediated by a cluster of basic residues at and around the canonical pT-docking site. Mutation of aprataxin FHA Arg29 prevented its interaction with MDC1 and recruitment to sites of DNA damage. These results indicate that aprataxin is involved not only in single strand break repair but also in the processing of a subset of double strand breaks presumably through its interaction with MDC1.