A new discovery of Neanderthal settlements in Turkey: Sürmecik open-air campsite in Western Anatolia

Western Anatolia is the poorest region in terms of Turkey's Palaeolithic finds. In the past years, only a few Palaeolithic artefacts were known from the surface in the provinces of İzmir, Manisa, Kütahya and Afyonkarahisar in western Anatolia. After the fossil Homo erectus skull fragment was found in the travertine deposits in Kocabaş (Denizli) in 2002, the importance of the region more increased. After this important discovery, Dr. Kadriye Özçelik started a Palaeolithic survey in Denizli and found a large number of chipped stone tools from the Lower and Middle Palaeolithic periods. Nevertheless, the last important Palaeolithic discovery in the region was made in Sürmecik (Banaz-Uşak) in 2015. This is an open-air campsite belonging to the Middle Palaeolithic period. Here is also a mining area where a mining operation is conducted. The chipped stone artefacts of the Sürmecik Palaeolithic open-air campsite come from a clay layer between hematite and limonite deposits under a travertine layer of about 4.5–5 meters in thickness. Faunal remains represent mostly by equids species. All stages of Mousterian culture are clearly visible in this open-air campsite. Sürmecik is the richest middle Palaeolithic open-air campsite in Turkey. The 83,002 lithic pieces were collected in the excavations carried out in 2016 and 2017. It is thought that the lithic assemblage will exceed 100,000 with the ongoing studies. The group of bifacial leaf points in this collection is seen in Turkey for the first time. Four master thesis studies started on the lithic material of Sürmecik. It is planned to take some samples for dating analysis along with ongoing studies.     

Dwellings and workspaces at Strandvägen, 5600–5000 cal. BC

This paper describes identified workspaces and the manufacture of slotted bone points at the Late Mesolithic settlement Strandvägen in Motala, in eastern central Sweden. Several dwellings were documented, Dwelling 1 being typically round-oval in shape 9 × 5.5 meters, with a floor area covering 49.5 m². Radiocarbon dates fall between approximately 5600-5200 cal BC. A combined archaeological record, with lithics and bone artefacts as well as analyses of the osteological assemblage has shown that slotted bone tools with mounted lithic inserts have been produced adjacent of the dwelling. The spatial distribution of bone flakes, microblades, processed resin and slotted artefacts testify to a clearly and delimited craft area near the shoreline of the river Motala Ström. Analyses of the finds, e.g. birch bark resin and prepared bone preforms by direct percussion, also help in reconstructing the stages of manufacturing composite projectile points in this part of Eurasia.     

Vibration attraction response is a plastic trait in blind Mexican tetra (Astyanax mexicanus), variable within subpopulations inhabiting the same cave

Animals evolve their sensory systems and foraging behaviours to adapt and colonize new and challenging habitats such as the dark cave environment. Vibration attraction behaviour (VAB) gives fish the ability to locate the source of a water disturbance in the darkness. VAB evolved in the blind Mexican cave tetra, Astyanax mexicanus. VAB is triggered in cavefish by vibration stimuli peaking at 35 Hz, which is within the main spectrum of water fluctuations produced by many prey crustaceans and insects. VAB has a genetic component and is correlated to an increased number of head mechanosensory neuromasts in the eye orbital region when compared to surface fish. Previous competitive prey capture assays have supported the advantage of VAB for foraging in the dark. Despite its putative adaptive function, VAB has been described as absent in some Astyanax cave populations (Tinaja and Molino) but present in others (Pachón, Piedras, Toro and Sabinos). Here we have tested the occurrence of VAB in the field and in multiple cave populations using a vibrating device in natural pools. Our results confirmed the presence of VAB in caves such as Pachón, Toro and Sabinos but showed that VAB is also present in the Tinaja and Molino cave populations, previously reported as VAB-negative in laboratory experiments. Thus, VAB is available throughout the range of hypogean A. mexicanus. However, and most notably, within a given cave the levels of VAB were highly variable among different pools. Fish at one pool may express no VAB, while fish at another nearby pool of the same cave may actively show VAB. While a variety of environmental conditions may foster this diversity, we found that individuals inhabiting pools with a high abundance of organic matter have reduced expression of VAB. In contrast, in pools with little organic debris where fish probably depend more on hunting than on scavenging, VAB is enhanced. Our results suggest that expression of VAB is a plastic trait whose variability can depend on local conditions. Such plasticity may be required within and among caves where high environmental variability between pools results in a diverse availability of food.     

Hidden areas of endemism: Small units in the South-eastern Neotropics

This study aimed to establish if the Lower Río de la Plata Basin (LRPB) wetlands can be considered a biogeographic unit. The species of this area were compiled and segregated according to the habitat, selecting only 87 endemic taxa restricted to the LRPB and linked to wetlands. Distributional data of species obtained from the literature, web databases, biological collections, and field trips were georeferenced. The areas of endemism were established as those areas where the distribution of two or more taxa overlaps in groups of rivers’ sections with geographic continuity and were tested with a cluster analysis. This congruence is due to ecological, geomorphological, and historical factors. Four areas of endemism were found: a broad area that comprises the whole study area (Riverine district), which is divided into three nested smaller areas (Paraguay–Paraná Flooding Valleys, Uruguay Basin, and Paraná Delta subdistricts). Then, we analysed 170 taxa distributions to evaluate the relationship between the study area and the neighbouring biogeographic units. According to the results, the study area belongs to the Paraná biogeographic province. Some areas of endemism are hidden inside broader areas and are hardly detected with the currently used biogeographic grid-methods. We propose to combine the information about ecological requirements of each taxon with its georeferenced records to estimate their areas of distribution as a primary step for searching areas of endemism in intracontinental studies.     

Investigating the origin of transoceanic distributions: Mtdna shows Mabuya lizards (Reptilia,Scincidae) crossed the Atlantic twice

Phylogenies with even a rough time scale can be used to investigate the history of non‐volant taxa with disjunct distributions in widely separated land areas that were once connected. Basic methods for doing this are discussed. A partial phylogeny of Mabuya based on mtDNA (305 bp cytochrome b, 379 bp 12S rRNA and 388 bp 16S rRNA) is used to show that this genus invaded tropical America from Africa twice in the last 9 Myr, once reaching the American mainland and once the oceanic island of Fernando de Noronha, two journeys each of at least 3000 km. In general, phylogenetic evidence for multiple invasions is less equivocal than that suggesting a single invasion, which is more prone to sampling artefacts. Two alternative hypotheses explaining the presence of Mabuya in both Africa and tropical America are refuted on the basis of molecular clock considerations, namely that the occurrence of Mabuya in these continents pre‐dated their separation over 100 My ago and that it was introduced from one continent to the other by human activities. Like several other lizard groups that have made successful long‐distance transmarine colonizations, Mabuya has done this on many occasions. Phylogenetic results are also compatible with a SE Asian or Australasian origin of Mabuya followed by westward expansion.     

Discovery,characterization, and remediation of a C-terminal Fc-extension in proteins expressed in CHO cells

ABSTRACT

Protein-based biotherapeutics are produced in engineered cells through complex processes and may contain a wide variety of variants and post-translational modifications that must be monitored or controlled to ensure product quality. Recently, a low level (~1–5%) impurity was observed in a number of proteins derived from stably transfected Chinese hamster ovary (CHO) cells using mass spectrometry. These molecules include antibodies and Fc fusion proteins where Fc is on the C-terminus of the construct. By liquid chromatography-mass spectrometry (LC-MS), the impurity was found to be ~1177 Da larger than the expected mass. After tryptic digestion and analysis by LC-MS/MS, the impurity was localized to the C-terminus of Fc in the form of an Fc sequence extension. Targeted higher-energy collision dissociation was performed using various normalized collision energies (NCE) on two charge states of the extended peptide, resulting in nearly complete fragment ion coverage. The amino acid sequence, SLSLSPEAEAASASELFQ, obtained by the de novo sequencing effort matches a portion of the vector sequence used in the transfection of the CHO cells, specifically in the promoter region of the selection cassette downstream of the protein coding sequence. The modification was the result of an unexpected splicing event, caused by the resemblance of the commonly used GGU codon of the C-terminal glycine to a consensus splicing donor. Three alternative codons for glycine were tested to alleviate the modification, and all were found to completely eliminate the undesirable C-terminal extension, thus improving product quality.     

De novo discovery of antibody drugs – great promise demands scrutiny

ABSTRACT

We live in an era of rapidly advancing computing capacity and algorithmic sophistication. “Big data” and “artificial intelligence”find progressively wider use in all spheres of human activity, including healthcare. A diverse array of computational technologies is being applied with increasing frequency to antibody drug research and development (R&D). Their successful applications are met with great interest due to the potential for accelerating and streamlining the antibody R&D process. While this excitement is very likely justified in the long term, it is less likely that the transition from the first use to routine practice will escape challenges that other new technologies had experienced before they began to blossom. This transition typically requires many cycles of iterative learning that rely on the deconstruction of the technology to understand its pitfalls and define vectors for optimization. The study by Vasquez et al. identifies a key obstacle to such learning: the lack of transparency regarding methodology in computational antibody design reports, which has the potential to mislead the community efforts