A diverse deep‐marine Ichnofauna from the Eocene Tarcau sandstone of the Eastern Carpathians,Romania

The Paleocene to Middle Eocene Tarcau Sandstone at Buzau Valley, eastern Carpathians, Romania, records sedimentation in a turbidite system. These strata contain a diverse and abundant pre‐ and postdepositional ichnofauna consisting of 35 ichnogenera and 54 ichnospecies. The predepositional assemblage is rich in graphoglyptids and ornate grazing trails; simple grazing trails, resting traces, and feeding structures also occur. The predepositional assemblage includes Acan‐thorhaphe, Belorhaphe, Cardioichnus, Circulichnus, Coch‐lichnus, Cosmorhaphe, Desmograpton, Fustiglyphus, Gordia, Helicolithus, Helminthopsis, Helminthorhaphe, Lorenzinia, Megagrapton, Paleodictyon, Paleomeandron, Protopaleodictyon, Scolicia (S. strozzii), Spirorhaphe, Spirophycus, Treptichnus, and Urohelminthoida. The ich‐nodiversity, composition, ethology, and morphologic complexity of the predepositional association are indicative of the Nereites ichnofacies. The postdepositional association essentially consists of dwelling, feeding, and grazing traces, and is represented by Chondrites, Glockerichnus, Halopoa, Nereites, Ophiomorpha, Phycodes, Planolites, Polykampton, Scolicia(S. prisca. S. striata), Taenidium, Thalassinoides, and Zoophycos. Palaeophycus occurs in both assemblages. Allochthonous Teredolites is present in wood fragments, The postdepositional association includes elements of the Skolithos ichnofacies and facies‐crossing forms that are commonly present in deep‐marine deposits, Elements of the Skolithos ichnofacies are present not only in the most proximal parts of the turbidite system, but also in distal parts. The number of predepositional forms greatly exceeds postdepositional ones, reflecting a dominance of K‐selected over r‐selected population strategies in a stable environment. High levels of ichnodiversity in the Tarcau Sandstone are comparable with deep‐sea ichnofaunas from the Polish Carpathians and with other flysch trace‐fossil assemblages of similar age. This abundant and diverse Eocene ichnofauna supports the idea of extremely rich deep‐sea ichnofaunas in the Cenozoic.     

Geospatial analysis of pollen records from the Yucatán peninsula, Mexico

Changes in distribution of semi-evergreen forest in the Yucatán peninsula and variation of precipitation during the late Holocene were inferred using a geographical information system. Deterministic methods for spatial interpolation using fossil pollen data from seven cores elucidated environmental changes. The changes in the distribution of the semi-evergreen forest allowed to us infer variations in precipitation in the area and to distinguish whether changes of forest cover are a consequence of climate and/or of human activities. The reconstruction of the Preclassic period (at 550 and 50 b.c.) indicates higher precipitation than at present and suggests a more closed vegetation cover. Around a.d. 450 the vegetation acquired an open character indicating a reduction in precipitation. During this time the decrease in forest was not homogeneous in the Yucatán peninsula, indicating human impacts in certain areas. A reduction in forest cover but not a complete deforestation of the region is assessed during the Classic period (a.d. 450). The reconstruction of a.d. 950 shows the recovery of the forest and is related to the Medieval warm period. Geographical information systems are useful tools to reconstruct the spatial history of the vegetation of the Yucatán peninsula during the late Holocene.     

An unusual brachiopod assemblage in a Late Jurassic (Kimmeridgian) stromatactis mud-mound of the Eastern Carpathians (Hăghimaş Mountains), Romania

An unusual fossil assemblage dominated by superabundant rhynchonellid brachiopods in a stromatactis mud-mound is recorded from the Hăghimaş Mountains (Eastern Carpathians), Romania. The mound mainly consists of bioclastic wackestones to packstones with a very rich macrofauna including crinoids, sponges, juvenile ammonites, and echinoids. The brachiopods represent a low-diversity but high-abundance association, dominated by the rhynchonellids Lacunosella and Septaliphoria. The taphonomical features of the fossil assemblage indicate an autochthonous fauna, with successive generations of brachiopods in life position and complete well-preserved individuals in different growth stage alongside an accessory population of crinoids and sponges. Brachiopod-brachiopod endosymbiotic life strategy is documented for the first time from a post-Paleozoic brachiopod assemblage. The mound reveals abundant stromatactis, filled by radiaxial fibrous or drusy calcite cement and internal polymud sediments. This is the first Late Jurassic (Kimmeridgian) stromatactis mud-mound identified in the Eastern Carpathians.     

Comprehensive analysis and characterization of the TCR α chain sequences in the common marmoset

The common marmoset (Callithrix jacchus) is useful as a nonhuman primate model of human diseases. Although the marmoset model has great potential for studying autoimmune diseases and immune responses against pathogens, little information is available regarding the genes involved in adaptive immunity. Here, we identified one TCR α constant (TRAC), 46 TRAJ (joining), and 35 TRAV (variable) segments from marmoset cDNA. Marmoset TRAC, TRAJ, and TRAV shared 80%, 68–100%, and 79–98% identity with their human counterparts at the amino acid level, respectively. The amino acid sequences were less conserved in TRAC than in TCRβ chain constant (TRBC). Comparative analysis of TRAV between marmosets and humans showed that the rates of synonymous substitutions per site (d _S ) were not significantly different between the framework regions (FRs) and complementarity determining regions (CDRs), whereas the rates of nonsynonymous substitutions per site (d _N ) were significantly lower in the FRs than in CDRs. Interestingly, the d _N values of the CDRs were greater for TRBV than TRAV. These results suggested that after the divergence of Catarrhini from Platyrrhini, amino acid substitutions were decreased in the FRs by purifying selection and occurred more frequently in CDRβ than in CDRα by positive selection, probably depending on structural and functional constraints. This study provides not only useful information facilitating the investigation of adaptive immunity using the marmoset model but also new insight into the molecular evolution of the TCR heterodimer in primate species.     

The history of settlement and agrarian land use in a boreal forest in Värmland,Sweden, new evidence from pollen analysis

Vegetation History and Archaeobotany - Shielings are the historically known form of transhumance in Scandinavia, where livestock were moved from the farmstead to sites in the outlands for summer...     

Distinguishing the effects of selection from demographic history in the genetic variation of two sister passerines based on mitochondrial–nuclear comparison

Determining the mechanisms responsible for the distribution of genetic diversity in natural populations has occupied a central role in molecular evolution. Our study was motivated by the unprecedented observation that a widespread Eurasian flycatcher, Ficedula albicilla, exhibited no variation at the mitochondrial DNA (mtDNA) ND2 gene in 75 individuals sampled over a 5000-km distance. In contrast, its sister species, F. parva, had low but considerably higher levels of mtDNA variation. We assessed whether natural selection or demographic factors could explain the absence of mtDNA variation in F. albicilla. Eighteen nuclear genes were sequenced to estimate the two species'' phylogeographic histories, and for comparison to the mtDNA data. Multilocus coalescence analyses suggested that F. albicilla experienced a population expansion perhaps following a population bottleneck. Simulations based on this demographic history, however, did not replicate the extremely low level of mtDNA variation. Historical range changes based on ecological niche models also failed to explain the observed mtDNA patterns. Neutrality tests (DHEW and ML-HKA) suggested a non-neutral pattern in the mtDNA of F. albicilla. We found a transmembrane-skewed distribution of nonsynonymous substitutions between the two species, three of which caused functional change; the results implied that positive selection could have targeted mtDNA. Several lines of evidence support selection rather than demographic history as the main force influencing the patterns of mtDNA variation. Despite the influence of natural selection, many of the phylogeographic inferences derived from mtDNA were robust, including species limits and a high level of gene flow among populations within species.     

Reflections on the use of interviews in the history of science: who will write the history of science?

Interviews are an excellent source of information for historians of science. They should be done by historians who understand science in detail and, if possible, better than the scientists they interview. In the case of applied industrial or governmental sciences, historians must have detailed knowledge of economic or historic sources. Again they should know more in these areas than those they interview. If, on the contrary, the interviewers are not scientists at heart who know science, the history they write will become at best literature but at worst pseudoscientific abracadabra.     

Genetic analysis of Turkish martens: Do two species of the genus Martes occur in Anatolia?

Stone marten (Martes foina) and European pine marten (M. martes) occur in western Eurasia. Current distributions of martens within Turkey and phylogenetic relationships among the Turkish and other populations of the two species within Eurasia remain relatively unknown. In this study, we aimed to determine genetic diversity within Martes populations inhabiting Turkey and to reveal the phylogenetic relationships among the Turkish and conspecific populations of the two marten species, using mitochondrial cytochrome b (CytB) sequences. Twenty‐four (24) haplotypes were identified among 86 marten samples collected across Turkey, including 23 novel haplotypes. Genetic distances among the Turkish haplotypes ranged from 0.1% to 0.8%, with an average of 0.3%. The 24 Turkish haplotypes were analysed together with those of conspecific populations deposited in GenBank. Phylogenetic (Bayesian Inference, maximum likelihood, neighbor‐joining) and network analyses revealed that all of the Turkish samples belonged to M. foina and that samples of M. martes were not encountered. Haplotypes of M. foina were divided into five haplogroups. The haplogroup including the two Chinese samples differed markedly from other the haplogroups. The remaining haplogroups contained samples from both the Turkish and European populations. We found that there was a genetically close relationship between the Turkish and the European stone marten populations. As a result of this study, M. martes may not be distributed in the Anatolian part of Turkey, possibly due to a barrier effect of two straits (Dardanelles and Bosporus) and the Caucasus Mountains. On the other hand, M. foina is distributed in both the Anatolian and Thracian parts of Turkey. Our results suggest that Turkey was likely one of the refuges for M. foina during Pleistocene glacial periods and is one of the centres of distribution of stone marten for Europe and the surrounding regions.     

Vegetation history and sea level variations during the last 13,500 years inferred from a pollen record at Chilika Lake,Orissa, India

Chilika Lake is the largest lagoon in Asia, situated in the state of Orissa in India. In the year 2000, many surface samples and cores were taken. Here the lithological results and especially those of the pollen analysis are shown. The oldest sediments of core CHI 9 were dated at about 13,500 cal years b.p. At this time the area of Chilika Lake was a river or a river delta with fresh water vegetation. With the increase in the sea level after about 9,500 cal years b.p. the area became an estuary with mangrove vegetation. Small variations in the sea level between about 5,000 and 2,500 cal years b.p. are not visible in our pollen profile. However the regression after about 2,000 cal years b.p. caused the formation of a barrier spit and sand ridges with the consequence that a big lagoon was formed, Chilika Lake. Marine influence diminished and the fresh water impact from the rivers increased. Mangrove vegetation disappeared and was replaced by fresh water vegetation. This paper is dedicated to Prof. Dr. Hans-Jürgen Beug on his 75th birthday.     

An Overview of the Ichnological and Ethological Studies in the Cave Bear Den in Urşilor Cave (Western Carpathians,Romania)

This paper presents a preliminary investigation of late Pleistocene cave bear traces from Ur?ilor Cave in the western Carpathians, Romania. The bears left thousands of traces on the walls, plateaus, and slopes of the cave interior. Some areas in the cave have been heavily trampled, leaving more than 140 hibernation beds as well as fur impressions. The footprints of cave bears are assigned to Ursichnus europaeus nov. ichnogen. and nov. ichnosp. and the cave bear-beds to Ursalveolus carpathicus nov. ichnogen. and nov. ichnosp. as behavioral traces. Tens of thousands of scratch marks on the slopes and top of a clay plateau are the result of bears moving from the hibernation area down to a stream and back. These traces reveal that the cave bears had short claws, similar to those of modern, primarily herbivorous black bears. Deep within the cave, three weathered, articulated cave bear skeletons still lie in their hibernation beds on the clay plateaus or a natural cave corner. One of these bears was a one-year-old male cub that did not survive its first hibernation; a second skeleton close was an adult female. The third, a young male, was found close to the end of the cave system. The bears of Ur?ilor Cave would have felt well protected against carnivores during their hibernation because their sleeping places were so deep within the cave. Their strategy may well have been to avoid any conflict with hyenas and lions during hibernation.     

Complementary DNA sequences of two 14.5 kDa subunits of NADH:ubiquinone oxidoreductase from bovine heart mitochondria. Completion of the primary structure of the complex?

The amino acid sequences of two nuclear-encoded subunits of complex I from bovine heart mitochondria have been determined. Both proteins have an apparent molecular weight of 14.5 kDa and their N-alpha-amino groups are acetylated. They are known as subunits B14.5a and B14.5b. Neither protein is evidently related to any known protein and their functions are obscure. A total of 34 nuclear-encoded subunits of bovine complex I have now been sequenced and it is thought that the primary structure of the complex is now complete, although with such a complicated structure it is difficult to be certain that there are no other subunits remaining to be sequenced. Seven additional hydrophobic subunits of the enzyme are encoded in mitochondrial DNA, and therefore bovine heart complex I is an assembly of about 41 different proteins. If it is assumed that there is one copy of each protein in the assembly, these polypeptides contain 7,955 amino acids in their sequences, more than are found in the Escherichia coli ribosome, which contains 7,336 amino acids in its 32 polypeptides.     

The start of the birch pollen season in Finnish Lapland: separating non‐local from local birch pollen and the implication for allergy sufferers

Determining the start of the birch pollen season requires the reliable separation of non‐local from locally produced birch pollen. The research was undertaken close to the latitudinal birch tree line at the Kevo Subarctic Research Institute (69°45′N 27°01′E) in northern Finland. By comparing phenological and aerobiological observations, the proportion of birch pollen present in the air before local anthesis commences can be delimited. We coupled this with data of pollen deposition monitored by means of a modified Tauber trap. The dominant birch species at Kevo is the mountain birch Betula pubescens ssp. czerepanovii, whereas B. pubescens ssp. pubescens is very rare, hence we consider the proportion of the southerly B. pubescens‐type pollen deposited in the pollen trap to be non‐local in origin.

We did not observe any trend towards an earlier start of the phenologically observed mountain birch anthesis at Kevo as predicted from work elsewhere. Moreover, the fixed 2.5% threshold method for determining the birch pollen season proved not to be applicable since in many years this threshold was reached before the end of continuous snow cover. The results indicate that in some years non‐local birch pollen contributes considerably to the allergen load in Lapland with up to 57% of the total birch pollen sum being recorded before the day on which local anthesis commenced, and up to 70% of the annual birch pollen deposited being of the southerly birch type.     

The life history of the tropical shad Tenualosa toli from Sarawak: first evidence of protandry in the Clupeiformes?

Synopsis Sharp declines in catches prompted a detailed study of the commercially and culturally important terubok Tenualosa toli, which lives in the fast-flowing, turbid estuaries and adjacent shallow coastal waters of Sarawak. Its reproduction, diet, age and growth were investigated. An absence of small females and large males, together with histological data showing transitional gonads, suggest that T. toli is a protandrous hermaphrodite. Ageing based on otoliths indicates that individuals may not live more than about two years. Male fish spawn towards the end of their first year, change sex (transitional gonads were recorded in fish from 14 to 31 cm SL) and spawn as females in their second year. Spawning takes place in the middle reaches of estuaries and females deposit all their eggs at once. Fecundity is linearly related to fish length but shows significant seasonal and site variations. Hermaphroditism is discussed in relation to possible environmental and isolating mechanisms. T. toli is a zooplanktivore eating mainly calanoid copepods. Laser-ablation inductively-coupled plasma mass spectroscopy of trace elements across otoliths revealed that the species does not move into full seawater or freshwater, but completes its life cycle in estuarine and adjacent coastal waters. Therefore T. toli populations in each estuary and adjacent coastal waters may be relatively isolated from one another, and hence particularly susceptible to overfishing.     

Pyroglutamate-Aβ: Role in the natural history of Alzheimer's disease

The accumulation of amyloid-beta (Aβ) peptides is believed to be a central contributor to the neurodegeneration typically seen in Alzheimer's disease (AD) brain. Aβ extracted from AD brains invariably possesses extensive truncations, yielding peptides of differing N- and C-terminal composition. Whilst Aβ is often abundant in the brains of cognitively normal elderly people, the brains of AD patients are highly enriched for N-terminally truncated Aβ bearing the pyroglutamate modification. Pyroglutamate-Aβ (pE-Aβ) has a higher propensity for oligomerisation and aggregation than full-length Aβ, potentially seeding the accumulation of neurotoxic Aβ oligomers and amyloid deposits. In addition, pE-Aβ has increased resistance to clearance by peptidases, causing these peptides to persist in biological fluids and tissues. The extensive deposition of pE-Aβ in human AD brain is under-represented in many transgenic mouse models of AD, reflecting major differences in the production and processing of Aβ peptides in these models compared to the human disease state.     

Approaching the taxonomic affiliation of unidentified sequences in public databases – an example from the mycorrhizal fungi

Background  

During the last few years, DNA sequence analysis has become one of the primary means of taxonomic identification of species, particularly so for species that are minute or otherwise lack distinct, readily obtainable morphological characters. Although the number of sequences available for comparison in public databases such as GenBank increases exponentially, only a minuscule fraction of all organisms have been sequenced, leaving taxon sampling a momentous problem for sequence-based taxonomic identification. When querying GenBank with a set of unidentified sequences, a considerable proportion typically lack fully identified matches, forming an ever-mounting pile of sequences that the researcher will have to monitor manually in the hope that new, clarifying sequences have been submitted by other researchers. To alleviate these concerns, a project to automatically monitor select unidentified sequences in GenBank for taxonomic progress through repeated local BLAST searches was initiated. Mycorrhizal fungi – a field where species identification often is prohibitively complex – and the much usedITSlocus were chosen as test bed.     

Molecular nature of β-Galactosidase from different tissues in two strains of the house mouse

One inbred mouse strain, C57BL/Kl, has high galactosidase activities in all tissues while another strain, DBA/2/Kl, has low activities determined by the Bgs locus. Beta-Galactosidase from these two strains was partly purified by a five-step procedure: acidification, ammonium sulfate precipitation, gel filtration at two pHs, and isoelectric focusing. No qualitative differences were found between the enzyme preparations from the two strains. They had identical heat inactivation curves, pH optima, molecular weight, and isoelectric points, and the Km values were very similar. It thus seems that this genetic difference in enzyme activity probably cannot be explained by a variation of the galactosidase-specific activity but rather reflects a difference in number of enzyme molecules. Eight different isoenzymes were separated from liver, kidney, and spleen. Each isoenzyme has a different electrophoretic mobility and there is a stepwise increase in molecular weight from 143,000 to 380,000 beginning with the protein having the lowest isoelectric point. A likely interpretation is that the isoenzymes bind a smaller polypeptide in varying numbers in addition to the enzymatic polypeptide per se.     

Salt-driven equilibrium between two conformations in the HAMP domain from Natronomonas pharaonis: the language of signal transfer?

HAMP domains (conserved in histidine kinases, adenylyl cyclases, methyl-accepting chemotaxis proteins, and phosphatases) perform their putative function as signal transducing units in diversified environments in a variety of protein families. Here the conformational changes induced by environmental agents, namely salt and temperature, on the structure and function of a HAMP domain of the phototransducer from Natronomonas pharaonis (NpHtrII) in complex with sensory rhodopsin II (NpSRII) were investigated by site-directed spin labeling electron paramagnetic resonance. A series of spin labeled mutants were engineered in NpHtrII157, a truncated analog containing only the first HAMP domain following the transmembrane helix 2. This truncated transducer is shown to be a valid model system for a signal transduction domain anchored to the transmembrane light sensor NpSRII. The HAMP domain is found to be engaged in a "two-state" equilibrium between a highly dynamic (dHAMP) and a more compact (cHAMP) conformation. The structural properties of the cHAMP as proven by mobility, accessibility, and intra-transducer-dimer distance data are in agreement with the four helical bundle NMR model of the HAMP domain from Archaeoglobus fulgidus.     

The history and rationale of using carbonic anhydrase inhibitors in the treatment of peptic ulcers. In memoriam Ioan Puşcaş (1932–2015)

Carbonic anhydrase (CA, EC 4.2.1.1) inhibitors (CAIs) started to be used in the treatment of peptic ulcers in the 1970s, and for more than two decades, a group led by Ioan Pu?ca? used them for this purpose, assuming that by inhibiting the gastric mucosa CA isoforms, hydrochloric acid secretion is decreased. Although acetazolamide and other sulfonamide CAIs are indeed effective in healing ulcers, the inhibition of CA isoforms in other organs than the stomach led to a number of serious side effects which made this treatment obsolete when the histamine H2 receptor antagonists and the proton pump inhibitors became available. Decades later, in 2002, it has been discovered that Helicobacter pylori, the bacterial pathogen responsible for gastric ulcers and cancers, encodes for two CAs, one belonging to the α-class and the other one to the β-class of these enzymes. These enzymes are crucial for the life cycle of the bacterium and its acclimation within the highly acidic environment of the stomach. Inhibition of the two bacterial CAs with sulfonamides such as acetazolamide, a low-nanomolar H. pylori CAI, is lethal for the pathogen, which explains why these compounds were clinically efficient as anti-ulcer drugs. Thus, the approach promoted by Ioan Pu?ca? for treating this disease was a good one although the rationale behind it was wrong. In this review, we present a historical overview of the sulfonamide CAIs as anti-ulcer agents, in memoriam of the scientist who was in the first line of this research trend.     

Historical presence of the sturgeon Acipenser sturio in the Rhône basin determined by the analysis of ancient DNA cytochrome b sequences

Sturgeon disappeared from the Rhône River in the mid 70’s without certitude about which species it was and about the existence of a sympatry between European sturgeon, Acipenser sturio, and Adriatic sturgeon, A. naccarii, in this watershed. In order to reach a reliable specific determination of this extinct sturgeon population, archaeozoological remains of the Jardin d’Hiver in Arles city, on the Rhône river banks, were genetically analysed, following strict criteria of authentication for the ancient DNA work. The rich collection of Arles sturgeon bone remains stems from human activities between the 6th and the 2nd Century BC. Sequences of 86 bp of the cytochrome b gene were obtained on four bones, from different anatomical parts of the fish and from different archaeological layers. All gave A. sturio diagnostic sequences. This preliminary analysis is an essential first step in the project of sturgeon reintroduction in the Rhône River. Thus, further analyses on a larger sample are necessary to comfort this result and to solve the question of sympatry with A. naccarii.