The genomes of two key bumblebee species with primitive eusocial organization

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The legs: a key to bird evolutionary success

Birds are the most diverse and largest group of extant tetrapods. They show marked variability, yet much of this variation is superficial and due to feather and bill color and shape. Under the feathers, the skeleto-muscular system is rather constant throughout the bird group. The adaptation to flight is the explanation for this uniformity. The more obvious morphological adaptations for flight are the wings, but the trunk is always rigid, the tail is short and the neck is flexible, since all these features are correlated with flying behaviour. Unrelated to the exigencies of flight, the legs always have three long bones, and all the birds walk on their toes. This leg structure is a striking plesiomorphic feature that was already present in related dinosaurs. The multi-purpose potential of the legs is the result of the skeletal architecture of a body with three segmented flexed legs. This configuration provides mechanical properties that allow the use of the legs as propulsive, paddling, foraging or grooming tools. It is the association of diverse modes of locomotion-walking, running, hopping, flying and swimming-that have enabled the birds to colonize almost all the environments on Earth.

Geological and hydrogeological features affecting migration, multi-phase partitioning and degradation of chlorinated hydrocarbons through unconsolidated porous media.

Chlorinated solvents are the most ubiquitous organic contaminants found in groundwater since the last five decades. They generally reach groundwater as Dense Non-Aqueous Phase Liquid (DNAPL). This phase can migrate through aquifers, and also through aquitards, in ways that aqueous contaminants cannot. The complex phase partitioning to which chlorinated solvent DNAPLs can undergo (i.e. to the dissolved, vapor or sorbed phase), as well as their transformations (e.g. degradation), depend on the physico-chemical properties of the contaminants themselves and on features of the hydrogeological system. The main goal of the thesis is to provide new knowledge for the future investigations of sites contaminated by DNAPLs in alluvial settings, proposing innovative investigative approaches and emphasizing some of the key issues and main criticalities of this kind of contaminants in such a setting. To achieve this goal, the hydrogeologic setting below the city of Ferrara (Po plain, northern Italy), which is affected by scattered contamination by chlorinated solvents, has been investigated at different scales (regional and site specific), both from an intrinsic (i.e. groundwater flow systems) and specific (i.e. chlorinated solvent DNAPL behavior) point of view. Detailed investigations were carried out in particular in one selected test-site, known as “Caretti site”, where high-resolution vertical profiling of different kind of data were collected by means of multilevel monitoring systems and other innovative sampling and analytical techniques. This allowed to achieve a deep geological and hydrogeological knowledge of the system and to reconstruct in detail the architecture of contaminants in relationship to the features of the hosting porous medium. The results achieved in this thesis are useful not only at local scale, e.g. employable to interpret the origin of contamination in other sites of the Ferrara area, but also at global scale, in order to address future remediation and protection actions of similar hydrogeologic settings.

Contiguous ∼16 Mb 1p36 deletion: Dominant features of classical distal 1p36 monosomy with haplo-lethality

Monosomy 1p36 results from heterozygous deletions of the terminal short chromosome 1 arm, the most common terminal deletion in humans. The microdeletion is split in two usually non-overlapping and clinically distinct classical distal and proximal 1p36 monosomy syndromes. Using comparative genome hybridization, MLPA and qPCR we identified the largest contiguous ∼16 Mb terminal 1p36 deletion reported to date. It covers both distal and proximal regions, causes a neonatally lethal variant with virtually exclusive features of distal 1p36 monosomy, highlighting the key importance of the gene-rich distal region for the "compound" 1p36 phenotype and a threshold deletion-size effect for haplo-lethality.

Glomerulonephropathy in Aged Captive Key Largo Woodrats (Neotoma floridana smalli)

A retrospective review of mortality records of Key Largo woodrats (Neotoma floridana smalli) in a captive breeding program revealed chronic renal disease in 5 of 6 woodrats older than 4 years of age. Two of the 5 woodrats with chronic renal disease also had clinical evidence of diabetes mellitus. Kidneys from all 5 woodrats were examined via light microscopy, histochemical staining, immunohistochemical staining, and transmission electron microscopy. The dietary histories of the affected animals were examined as well. The most striking histopathologic abnormality in the affected kidneys was the presence of large protein casts within cortical and medullary tubules in combination with lesions of membranous glomerulopathy and glomerulosclerosis. Transmission electron microscopy revealed thickening and undulation of the tubular and glomerular mesangial basement membranes with the variable presence of electron-dense deposits within the capillary endothelial basement membrane. Patchy glomerular immunoreactivity for IgG was noted in 2 cases, but IgA and IgM immunoreactivity were not present. The pathologic changes in the kidneys of the Key Largo woodrats mirrored many of the features of chronic progressive nephropathy commonly diagnosed in laboratory rats. Woodrats in the captive population were fed an ad libitum high-protein diet similar to diets that have been shown in laboratory rats to exacerbate the development and progression of chronic progressive nephropathy. It is concluded that Key Largo woodrats develop glomerulonephropathy with features similar to chronic progressive nephropathy described in laboratory rats. Age, concomitant disease, and dietary factors may contribute to the development and severity of this potentially age-limiting disease in Key Largo woodrats.

Study protocol: Transition from localized low back pain to chronic widespread pain in general practice: identification of risk factors, preventive factors and key elements for treatment--a cohort study

Background Chronic localized pain syndromes, especially chronic low back pain (CLBP), are common reasons for consultation in general practice. In some cases chronic localized pain syndromes can appear in combination with chronic widespread pain (CWP). Numerous studies have shown a strong association between CWP and several physical and psychological factors. These studies are population-based cross-sectional and do not allow for assessing chronology. There are very few prospective studies that explore the predictors for the onset of CWP, where the main focus is identifying risk factors for the CWP incidence. Until now there have been no studies focusing on preventive factors keeping patients from developing CWP. Our aim is to perform a cross sectional study on the epidemiology of CLBP and CWP in general practice and to look for distinctive features regarding resources like resilience, self-efficacy and coping strategies. A subsequent cohort study is designed to identify the risk and protective factors of pain generalization (development of CWP) in primary care for CLBP patients. Methods/Design Fifty-nine general practitioners recruit consecutively, during a 5 month period, all patients who are consulting their family doctor because of chronic low back pain (where the pain is lasted for 3 months). Patients are asked to fill out a questionnaire on pain anamnesis, pain-perception, co-morbidities, therapy course, medication, socio demographic data and psychosomatic symptoms. We assess resilience, coping resources, stress management and self-efficacy as potential protective factors for pain generalization. Furthermore, we raise risk factors for pain generalization like anxiety, depression, trauma and critical life events. During a twelve months follow up period a cohort of CLBP patients without CWP will be screened on a regular basis (3 monthly) for pain generalization (outcome: incident CWP). Discussion This cohort study will be the largest study which prospectively analyzes predictors for transition from CLBP to CWP in primary care setting. In contrast to the typically researched risk factors, which increase the probability of pain generalization, this study also focus intensively on protective factors, which decrease the probability of pain generalization.

Study design features affecting outcome in antidepressant trials

A key issue in the approval process of antidepressants is the inconsistency of results between antidepressant clinical phase III trials. Identifying factors influencing efficacy data is needed to facilitate interpretation of the results.

Contrasts, Contacts, and Interconnections — Tel Kinrot as an Early Iron Age Key Site in the Northern Jordan Rift Valley at the Dawn of the 1st Millennium BCE

Ancient Kinneret (Tēl Kinrōt [Hebrew]; Tell el-ʿOrēme [Arabic]) is located on a steep limestone hill on the northwestern shores of the Sea of Galilee (2508.7529 [NIG]). The site, whose settlement history began sometime during the Pottery-Neolithic or the early Chalcolithic period, is emerging as one of the major sites for the study of urban life in the Southern Levant during the Early Iron Age (c. 1130–950 BCE). Its size, accessibility by major trade routes, and strategic location between different spheres of cultural and political influence make Tēl Kinrōt an ideal place for studying the interaction of various cultures on urban sites, as well as to approach questions of ethnicity and regionalism during one of the most debated periods in the history of the ancient Levant. The paper will briefly discuss the settlement history of the site during the Early Iron Age. However, the main focus will lie on the material culture of the late Iron Age IB city that rapidly evolved to a regional center during the transition from the 11th to the 10th century BCE. During this period, ancient Kinneret features a multitude of cultural influences that reach from Egypt via the Central Hill Country until the Northern parts of Syria and the Amuq region. While there are indisputably close ties with the ‘Aramaean’ realm, there are also strong indications that there were – at the same time – vivid socio-economic links with the West, i.e. the Southern and Northern Mediterranean coasts and their hinterland. It will be argued that the resulting ‘cultural blend’ is a typical characteristic of the material culture of the Northern Jordan Rift Valley in the advent of the emerging regional powers of the Iron Age II.

Proteomic analysis of the Plasmodium male gamete reveals the key role for glycolysis in flagellar motility

BACKGROUND Gametogenesis and fertilization play crucial roles in malaria transmission. While male gametes are thought to be amongst the simplest eukaryotic cells and are proven targets of transmission blocking immunity, little is known about their molecular organization. For example, the pathway of energy metabolism that power motility, a feature that facilitates gamete encounter and fertilization, is unknown. METHODS Plasmodium berghei microgametes were purified and analysed by whole-cell proteomic analysis for the first time. Data are available via ProteomeXchange with identifier PXD001163. RESULTS 615 proteins were recovered, they included all male gamete proteins described thus far. Amongst them were the 11 enzymes of the glycolytic pathway. The hexose transporter was localized to the gamete plasma membrane and it was shown that microgamete motility can be suppressed effectively by inhibitors of this transporter and of the glycolytic pathway. CONCLUSIONS This study describes the first whole-cell proteomic analysis of the malaria male gamete. It identifies glycolysis as the likely exclusive source of energy for flagellar beat, and provides new insights in original features of Plasmodium flagellar organization.

Dialect features indexing hipster identity on social media: the case of the city of Malaga

Identity is a recurrent research interest in current sociolinguistics and it is also of primary interest in digital discourse studies. Identity construction is closely related to stance and style (Eckert 2008; Jaffe 2009), which are fundamental concepts for understanding the language use and its social meanings in the case of social media users from Malaga. As the specific social meanings of a set of dialect features constitute a style, this style and the social (and technological) context in which the variants are used determine the meanings that are actually associated with each variant. Hence, every variant has its own indexical field covering any number of potential meanings. The Spanish spoken in Malaga, as Andalusian Spanish in general, was in the past often times considered an incorrect, low prestige variety of Spanish which was strongly associated with the poor, rural, backward South of Spain. This southern Spanish variety is easily recognised because of its innovative phonetic features that diverge from the national standard. In this study several of these phonetic dialect features are looked at, which users from Malaga purposefully employ (in a textualised form) on social media for identity construction. This identity construction is analysed through interactional and ethnographic methods: A perception and an imitation task served as key data and were supplemented by answers to a series of open questions. Further data stems from visual, multimodal elements (e.g. images, photos, videos) posted by users from the city of Malaga. The program TAMS Analyzer was used for data codification and analysis. Results show that certain features that in spoken language are considered rural and old-fashioned, acquire new meaning on social media, namely of urbanity and fashion. Moreover, these features, if used online, are associated with hipsters. That is, the “cool” social media index the “coolness” of the dialect features in question and, thus, the mediatisation makes their indexical fields even more multi-layered and dynamic. Social media users from Malaga performatively employ these stylised dialect features to project a hipster identity and certain related stances.

The Japan-Peru FTA : antecedents, significance and main features

The Economic Partnership Agreement (EPA) between Japan and Peru came into effect on March 1, 2012. This paper provides background information about this agreement's significance, mostly from a Peruvian point of view. It focuses on the following subjects: the statistical trends showing Peru's declining shares in Japan's trade and investment flows with Latin American countries between the mid-1970s and mid-2000s, the main explanatory factors of such a deterioration in Peru's economic position over that period, the changes of trade policy strategy in both countries since the 2000s, and the EPA negotiation process and some of its key results as featured in the text of the agreement.

Including functional usability features in a Model-Driven Development Method

The Software Engineering (SE) community has historically focused on working with models to represent functionality and persistence, pushing interaction modelling into the background, which has been covered by the Human Computer Interaction (HCI) community. Recently, adequately modelling interaction, and specifically usability, is being considered as a key factor for success in user acceptance, making the integration of the SE and HCI communities more necessary. If we focus on the Model-Driven Development (MDD) paradigm, we notice that there is a lack of proposals to deal with usability features from the very first steps of software development process. In general, usability features are manually implemented once the code has been generated from models. This contradicts the MDD paradigm, which claims that all the analysts? effort must be focused on building models, and the code generation is relegated to model to code transformations. Moreover, usability features related to functionality may involve important changes in the system architecture if they are not considered from the early steps. We state that these usability features related to functionality can be represented abstractly in a conceptual model, and their implementation can be carried out automatically.

Protein thermostability above 100°C: A key role for ionic interactions

The discovery of hyperthermophilic microorganisms and the analysis of hyperthermostable enzymes has established the fact that multisubunit enzymes can survive for prolonged periods at temperatures above 100°C. We have carried out homology-based modeling and direct structure comparison on the hexameric glutamate dehydrogenases from the hyperthermophiles Pyrococcus furiosus and Thermococcus litoralis whose optimal growth temperatures are 100°C and 88°C, respectively, to determine key stabilizing features. These enzymes, which are 87% homologous, differ 16-fold in thermal stability at 104°C. We observed that an intersubunit ion-pair network was substantially reduced in the less stable enzyme from T. litoralis, and two residues were then altered to restore these interactions. The single mutations both had adverse effects on the thermostability of the protein. However, with both mutations in place, we observed a fourfold improvement of stability at 104°C over the wild-type enzyme. The catalytic properties of the enzymes were unaffected by the mutations. These results suggest that extensive ion-pair networks may provide a general strategy for manipulating enzyme thermostability of multisubunit enzymes. However, this study emphasizes the importance of the exact local environment of a residue in determining its effects on stability.

CKAAPs DB: a conserved key amino acid positions database

The Conserved Key Amino Acid Positions DataBase (CKAAPs DB) provides access to an analysis of structurally similar proteins with dissimilar sequences where key residues within a common fold are identified. The derivation and significance of CKAAPs starting from pairwise structure alignments is described fully in Reddy et al. [Reddy,B.V.B., Li,W.W., Shindyalov,I.N. and Bourne,P.E. (2000) Proteins, in press]. The CKAAPs identified from this theoretical analysis are provided to experimentalists and theoreticians for potential use in protein engineering and modeling. It has been suggested that CKAAPs may be crucial features for protein folding, structural stability and function. Over 170 substructures, as defined by the Combinatorial Extension (CE) database, which are found in approximately 3000 representative polypeptide chains have been analyzed and are available in the CKAAPs DB. CKAAPs DB also provides CKAAPs of the representative set of proteins derived from the CE and FSSP databases. Thus the database contains over 5000 representative poly­peptide chains, covering all known structures in the PDB. A web interface to a relational database permits fast retrieval of structure-sequence alignments, CKAAPs and associated statistics. Users may query by PDB ID, protein name, function and Enzyme Classification number. Users may also submit protein alignments of their own to obtain CKAAPs. An interface to display CKAAPs on each structure from a web browser is also being implemented. CKAAPs DB is maintained by the San Diego Supercomputer Center and accessible at the URL http://ckaaps.sdsc.edu.

The Early Miocene “Bisciaro volcaniclastic event” (northern Apennines, Italy): a key study for the geodynamic evolution of the central-western Mediterranean

The Early Miocene Bisciaro Fm., a marly limestone succession cropping out widely in the Umbria–Romagna–Marche Apennines, is characterized by a high amount of volcaniclastic content, characterizing this unit as a peculiar event of the Adria Plate margin. Because of this volcaniclastic event, also recognizable in different sectors of the central-western Mediterranean chains, this formation is proposed as a “marker” for the geodynamic evolution of the area. In the Bisciaro Fm., the volcaniclastic supply starts with the “Raffaello” bed (Earliest Aquitanian) that marks the base of the formation and ends in the lower portion of the Schlier Fm. (Late Burdigalian–Langhian p.p.). Forty-one studied successions allowed the recognition of three main petrofacies: (1) Pyroclastic Deposits (volcanic materials more than 90 %) including the sub-petrofacies 1A, Vitroclastic/crystallo-vitroclastic tuffs; 1B, Bentonitic deposits; and 1C, Ocraceous and blackish layers; (2) Resedimented Syn-Eruptive Volcanogenic Deposits (volcanic material 30–90 %) including the sub-petrofacies 2A, High-density volcanogenic turbidites; 2B, Low-density volcanogenic turbidites; 2C, Crystal-rich volcanogenic deposits; and 2D, Glauconitic-rich volcaniclastites; (3) Mixing of Volcaniclastic Sediments with Marine Deposits (volcanic material 5–30 %, mixed with marine sediments: marls, calcareous marls, and marly limestones). Coeval volcaniclastic deposits recognizable in different tectonic units of the Apennines, Maghrebian, and Betic Chains show petrofacies and chemical–geochemical features related to a similar calc-alkaline magmatism. The characterization of this event led to the hypothesis of a co-genetic relationship between volcanic activity centres (primary volcanic systems) and depositional basins (depositional processes) in the Early Miocene palaeogeographic and palaeotectonic evolution of the central-western Mediterranean region. The results support the proposal of a geodynamic model of this area that considers previously proposed interpretations.