Stratigraphic reassessment of Grotta Romanelli sheds light on Middle-Late Pleistocene palaeoenvironments and human settling in the Mediterranean.

During the last century, Grotta Romanelli (Southern Italy) has been a reference site for the European Late Pleistocene stratigraphy, due to its geomorphological setting and archaeological and palaeontological content. The beginning of the sedimentation inside the cave was attributed to the Last Interglacial (MISs 5e) and the oldest unearthed evidence of human occupation, including remains of hearths, was therefore referred to the Middle Palaeolithic. Recent surveys and excavations produced new U/Th dates, palaeoenvironmental interpretation and a litho-, morpho- and chrono-stratigraphical reassessment, placing the oldest human frequentation of the cave between MIS 9 and MIS 7, therefore embracing Glacial and Interglacial cycles. These new data provide evidence that the sea reached the cave during the Middle Pleistocene and human occupation occurred long before MISs 5e and persisted beyond the Pleistocene- Holocene boundary.

A Middle Pleistocene wolf from central Italy provides insights on the first occurrence of Canis lupus in Europe.

Here, we describe a partial cranium of a large canid dated at 406.5 ± 2.4 ka from the Middle Pleistocene of Ponte Galeria (Rome, Italy). The sample represents one of the few Middle Pleistocene remains of a wolf-like canid falling within the timeframe when the Canis mosbachensis-Canis lupus transition occurred, a key moment to understand the spread of the extant wolf (Canis lupus) in Europe. CT-based methods allow studying the outer and inner cranial anatomy (brain and frontal sinuses) of a selected sample of fossil and extant canids. Morphological and biometric results allowed to: (I) ascribe the cranium from Ponte Galeria to an adult Canis lupus, representing the first reliable occurrence of this taxon in Europe; (II) provide the content for a biochronological revision of the Middle Pleistocene record of European wolves.

Cobalt-catalyzed cross-coupling reactions of aryl- and alkylaluminum derivatives with (hetero)aryl and alkyl bromides.

A simple cobalt complex, such as Co(phen)Cl2, turned out to be a highly efficient and cheap precatalyst for a host of cross-coupling reactions involving aromatic and aliphatic organoaluminum reagents with aryl, heteroaryl and alkyl bromides. New C(sp2)-C(sp2) and C(sp2)-C(sp3) bonds were formed in good to excellent yields and with high chemoselectivity, under mild reaction conditions.

Perception of Social Odor and Gender-Related Differences Investigated Through the Use of Transfer Entropy and Embodied Medium.

The perception of putative pheromones or social odors (PPSO) in humans is a widely debated topic because the published results seem ambiguous. Our research aimed to evaluate how cross-modal processing of PPSO and gender voice can affect the behavioral and psychophysiological states of the subject during a listening task with a bodily contact medium, and how these effects could be gender related. Before the experimental session, three embodied media, were exposed to volatilized estratetraenol (Estr), 5α-androst-16-en-3 α-ol (Andr), and Vaseline oil. The experimental session consisted in listening to a story that were transmitted, with a male or female voice, by the communicative medium via a Bluetooth system during a listening task, recorded through 64-active channel electroencephalography (EEG). The sense of co-presence and social presence, elicited by the medium, showed how the established relationship with the medium was gender dependent and modulated by the PPSO. In particular, Andr induced greater responses related to co-presence. The gender of the participants was related to the co-presence desire, where women imagined higher medium co-presence than men. EEG findings seemed to be more responsive to the PPSO-gender voice interaction, than behavioral results. The mismatch between female PPSO and male voice elicited the greatest cortical flow of information. In the case of the Andr-male voice condition, the trained model appeared to assign more relevance to the flow of information to the right frontotemporal regions (involved in odor recognition memory and social behavior). The Estr-male voice condition showed activation of the bilateral frontoparietal network, which is linked to cognitive control, cognitive flexibility, and auditory consciousness. The model appears to distinguish the dissonance condition linked to Andr matched with a female voice: it highlights a flow of information to the right occipital lobe and to the frontal pole. The PPSO could influence the co-presence judgements and EEG response. The results seem suggest that could be an implicit pattern linked to PPSO-related gender differences and gender voice.

RNA-Seq read alignments with PALMapper.

Next-generation sequencing technologies have revolutionized genome and transcriptome sequencing. RNA-Seq experiments are able to generate huge amounts of transcriptome sequence reads at a fraction of the cost of Sanger sequencing. Reads produced by these technologies are relatively short and error prone. To utilize such reads for transcriptome reconstruction and gene-structure identification, one needs to be able to accurately align the sequence reads over intron boundaries. In this unit, we describe PALMapper, a fast and easy-to-use tool that is designed to accurately compute both unspliced and spliced alignments for millions of RNA-Seq reads. It combines the efficient read mapper GenomeMapper with the spliced aligner QPALMA, which exploits read-quality information and predictions of splice sites to improve the alignment accuracy. The PALMapper package is available as a command-line tool running on Unix or Mac OS X systems or through a Web interface based on Galaxy tools.

mGene: accurate SVM-based gene finding with an application to nematode genomes.

We present a highly accurate gene-prediction system for eukaryotic genomes, called mGene. It combines in an unprecedented manner the flexibility of generalized hidden Markov models (gHMMs) with the predictive power of modern machine learning methods, such as Support Vector Machines (SVMs). Its excellent performance was proved in an objective competition based on the genome of the nematode Caenorhabditis elegans. Considering the average of sensitivity and specificity, the developmental version of mGene exhibited the best prediction performance on nucleotide, exon, and transcript level for ab initio and multiple-genome gene-prediction tasks. The fully developed version shows superior performance in 10 out of 12 evaluation criteria compared with the other participating gene finders, including Fgenesh++ and Augustus. An in-depth analysis of mGene's genome-wide predictions revealed that approximately 2200 predicted genes were not contained in the current genome annotation. Testing a subset of 57 of these genes by RT-PCR and sequencing, we confirmed expression for 24 (42%) of them. mGene missed 300 annotated genes, out of which 205 were unconfirmed. RT-PCR testing of 24 of these genes resulted in a success rate of merely 8%. These findings suggest that even the gene catalog of a well-studied organism such as C. elegans can be substantially improved by mGene's predictions. We also provide gene predictions for the four nematodes C. briggsae, C. brenneri, C. japonica, and C. remanei. Comparing the resulting proteomes among these organisms and to the known protein universe, we identified many species-specific gene inventions. In a quality assessment of several available annotations for these genomes, we find that mGene's predictions are most accurate.

Optimal spliced alignments of short sequence reads.

MOTIVATION: Next generation sequencing technologies open exciting new possibilities for genome and transcriptome sequencing. While reads produced by these technologies are relatively short and error prone compared to the Sanger method their throughput is several magnitudes higher. To utilize such reads for transcriptome sequencing and gene structure identification, one needs to be able to accurately align the sequence reads over intron boundaries. This represents a significant challenge given their short length and inherent high error rate. RESULTS: We present a novel approach, called QPALMA, for computing accurate spliced alignments which takes advantage of the read's quality information as well as computational splice site predictions. Our method uses a training set of spliced reads with quality information and known alignments. It uses a large margin approach similar to support vector machines to estimate its parameters to maximize alignment accuracy. In computational experiments, we illustrate that the quality information as well as the splice site predictions help to improve the alignment quality. Finally, to facilitate mapping of massive amounts of sequencing data typically generated by the new technologies, we have combined our method with a fast mapping pipeline based on enhanced suffix arrays. Our algorithms were optimized and tested using reads produced with the Illumina Genome Analyzer for the model plant Arabidopsis thaliana. AVAILABILITY: Datasets for training and evaluation, additional results and a stand-alone alignment tool implemented in C++ and python are available at http://www.fml.mpg.de/raetsch/projects/qpalma.