Limited dispersal and local adaptation promote allopatric speciation in a biodiversity hotspot

Recently diverged or diverging populations can offer unobstructed insights into early barriers to gene flow during the initial stages of speciation. The current study utilised a novel insect system (order Mantophasmatodea) to shed light on the early drivers of speciation. The members of this group have limited dispersal abilities, small allopatric distributions and strong habitat associations in the Cape Floristic Region biodiversity hotspot in South Africa. Sister taxa from the diverse family Austrophasmatidae were chosen as focal species (Karoophasma biedouwense, K. botterkloofense). Population genetics and Generalized Dissimilarity Modelling (GDM) were used to characterise spatial patterns of genetic variation and evaluate the contribution of environmental factors to population divergence and speciation. Extensive sampling confirmed the suspected allopatry of these taxa. However, hybrids were identified in a narrow region occurring between the species' distributions. Strong population structure was found over short geographic distances; particularly in K. biedouwense in which geographic distance accounted for 32% of genetic variation over a scale of 50 km (r = .56, p < .001). GDM explained 42%–78% of the deviance in observed genetic dissimilarities. Geographic distance was consistently indicated to be important for between species and within population differentiation, suggesting that limited dispersal ability may be an important neutral driver of divergence. Temperature, altitude, precipitation and vegetation were also indicated as important factors, suggesting the possible role of adaptation to local environmental conditions for species divergence. The discovery of the hybrid-zone, and the multiple allopatric species pairs in Austrophasmatidae support the idea that this could be a promising group to further our understanding of speciation modes.     

Is Coal Fly Ash a Suitable Alkaline Resource for Manufacturing New Calcium Carbonate–based Cements? A Systems Analytical Evaluation

At present, the production of cement contributes approximately 8% to global carbon dioxide (CO₂) emissions, whereas a further increase in the future is expected. To reduce these emissions, a prominent measure of the cement industry is to use materials such as coal fly ash (CFA) as a cement substitute, but the availability of qualified ash is limited. The development of “green cements” with lower CO₂ emissions attracts attention within the cement industry and politics. Recently, a new invention for a calcium carbonate (CaCO₃)‐based cement intends to use CFA as an alkaline resource during a manufacturing process based on CO₂ mineralization converting anthropogenic CO₂ into stable calcareous materials by using calcium‐bearing brines. In our systems analysis, we demonstrate that the alkalinity of CFA usable for mass production of cements is poor. The alkalinity of CFA primarily depends on the dissolution of free lime. For CO₂ mineralization, the resulting alkalinity is just sufficient to precipitate the calcium supplied by the CFA itself, and the capacity of CO₂ mineralization is low. Thus, CFA could only be used as a supplementary resource. Even at locations where exceptional calcium‐rich ash is available, very large amounts of ash must be processed. Globally, only a few million tonnes of calcium could be extracted in this way. Because qualified CFA is already used in the construction industry, the extraction of calcium from nonqualified, more polluted CFA is associated with a risk of unwanted environmental effects and implies an elaborated pollutant control.     

Changes of 25-OH-Vitamin D during Overwintering at the German Antarctic Stations Neumayer II and III

Purpose

Humans in Antarctica face different environmental challenges, such as low ultra-violet radiation, which is crucial for vitamin D production in humans. Therefore we assessed changes in 25-OH-vitamin D serum concentration during 13 months of overwintering at the German Stations Neumayer II and III (2007–2012). We hypothesized that (i) 25-OH-vitamin D serum concentration would significantly decrease, (ii) changes would be affected by age, gender, baseline (i.e. pre-overwintering) fat mass, baseline 25-OH-vitamin D serum concentration, and station residence, and (iii) our results would not differ from similar previous studies in comparable high latitudes.

Materials & Methods

25-OH-vitamin D serum concentrations were determined before, after, and monthly during the campaigns from venous blood samples of n = 43 participants (28 men, 15 women). Baseline fat mass was determined via bio impedance analysis and body plethysmography. Data were analyzed for change over time, dependency on independent parameters, and after categorization for sufficiency (>50nmol/l), insufficiency (25-50nmol/l), and deficiency (<25nmol/l). Results were compared with data from similar previous studies.

Results

We found a significant decrease of 25-OH-vitamin D with dependency on month. Age, gender, fat mass, and station residence had no influence. Only baseline 25-OH-vitamin D serum concentrations significantly affected subsequent 25-OH-vitamin D values.

Conclusions

Overwinterings at the Antarctic German research stations Neumayer II and III are associated with a decrease in 25-OH-vitamin D serum concentrations, unaffected by age, gender, baseline fat mass, and station residence. Higher baseline vitamin D serum concentrations might protect from subsequent deficiencies. Residence at the Neumayer Stations may lead to lower vitamin D serum concentrations than found in other comparable high latitudes.     

Tilt Table Therapies for Patients with Severe Disorders of Consciousness: A Randomized,Controlled Trial

One major aim of the neurological rehabilitation of patients with severe disorders of consciousness (DOC) is to enhance patients’ arousal and ability to communicate. Mobilization into a standing position by means of a tilt table has been shown to improve their arousal and awareness. However, due to the frequent occurrence of syncopes on a tilt table, it is easier to accomplish verticalization using a tilt table with an integrated stepping device. The objective of this randomized controlled clinical trial was to evaluate the effectiveness of a tilt table therapy with or without an integrated stepping device on the level of consciousness. A total of 50 participants in vegetative or minimally conscious states 4 weeks to 6 month after injury were treated with verticalization during this randomized controlled trial. Interventions involved ten 1-hour sessions of the specific treatment over a 3-week period. Blinded assessors made measurements before and after the intervention period, as well as after a 3-week follow-up period. The coma recovery scale-revised (CRS-R) showed an improvement by a median of 2 points for the group receiving tilt table with integrated stepping (Erigo). The rate of recovery of the group receiving the conventional tilt table therapy significantly increased by 5 points during treatment and by an additional 2 points during the 3-week follow-up period. Changes in spasticity did not significantly differ between the two intervention groups. Compared to the conventional tilt table, the tilt table with integrated stepping device failed to have any additional benefit for DOC patients. Verticalization itself seems to be beneficial though and should be administered to patients in DOC in early rehabilitation. Trial Registration: Current Controlled Trials Ltd (www.controlled-trials.com), identifier number ISRCTN72853718     

Safety and Efficacy of At-Home Robotic Locomotion Therapy in Individuals with Chronic Incomplete Spinal Cord Injury: A Prospective,Pre-Post Intervention,Proof-of-Concept Study

Background

The compact Motorized orthosis for home rehabilitation of Gait (MoreGait) was developed for continuation of locomotion training at home. MoreGait generates afferent stimuli of walking with the user in a semi-supine position and provides feedback about deviations from the reference walking pattern.

Objective

Prospective, pre-post intervention, proof-of-concept study to test the feasibility of an unsupervised home-based application of five MoreGait prototypes in subjects with incomplete spinal cord injury (iSCI).

Methods

Twenty-five (5 tetraplegia, 20 paraplegia) participants with chronic (mean time since injury: 5.8 ± 5.4 (standard deviation, SD) years) sensorimotor iSCI (7 ASIA Impairment Scale (AIS) C, 18 AIS D; Walking Index for Spinal Cord Injury (WISCI II): Interquartile range 9 to 16) completed the training (45 minutes / day, at least 4 days / week, 8 weeks). Baseline status was documented 4 and 2 weeks before and at training onset. Training effects were assessed after 4 and 8 weeks of therapy.

Results

After therapy, 9 of 25 study participants improved with respect to the dependency on walking aids assessed by the WISCI II. For all individuals, the short-distance walking velocity measured by the 10-Meter Walk Test showed significant improvements compared to baseline (100%) for both self-selected (Mean 139.4% ± 35.5% (SD)) and maximum (Mean 143.1% ± 40.6% (SD)) speed conditions as well as the endurance estimated with the six-minute walk test (Mean 166.6% ± 72.1% (SD)). One device-related adverse event (pressure sore on the big toe) occurred in over 800 training sessions.

Conclusions

Home-based robotic locomotion training with MoreGait is feasible and safe. The magnitude of functional improvements achieved by MoreGait in individuals with iSCI is well within the range of complex locomotion robots used in hospitals. Thus, unsupervised MoreGait training potentially represents an option to prolong effective training aiming at recovery of locomotor function beyond in-patient rehabilitation.

Trial Registration

German Clinical Trials Register (DKRS) DRKS00005587     

Genomic Heterogeneity of Osteosarcoma - Shift from Single Candidates to Functional Modules

Osteosarcoma (OS), a bone tumor, exhibit a complex karyotype. On the genomic level a highly variable degree of alterations in nearly all chromosomal regions and between individual tumors is observable. This hampers the identification of common drivers in OS biology. To identify the common molecular mechanisms involved in the maintenance of OS, we follow the hypothesis that all the copy number-associated differences between the patients are intercepted on the level of the functional modules. The implementation is based on a network approach utilizing copy number associated genes in OS, paired expression data and protein interaction data. The resulting functional modules of tightly connected genes were interpreted regarding their biological functions in OS and their potential prognostic significance. We identified an osteosarcoma network assembling well-known and lesser-known candidates. The derived network shows a significant connectivity and modularity suggesting that the genes affected by the heterogeneous genetic alterations share the same biological context. The network modules participate in several critical aspects of cancer biology like DNA damage response, cell growth, and cell motility which is in line with the hypothesis of specifically deregulated but functional modules in cancer. Further, we could deduce genes with possible prognostic significance in OS for further investigation (e.g. EZR, CDKN2A, MAP3K5). Several of those module genes were located on chromosome 6q. The given systems biological approach provides evidence that heterogeneity on the genomic and expression level is ordered by the biological system on the level of the functional modules. Different genomic aberrations are pointing to the same cellular network vicinity to form vital, but already neoplastically altered, functional modules maintaining OS. This observation, exemplarily now shown for OS, has been under discussion already for a longer time, but often in a hypothetical manner, and can here be exemplified for OS.     

Analysis of Phosphorylation-dependent Protein Interactions of Adhesion and Degranulation Promoting Adaptor Protein (ADAP) Reveals Novel Interaction Partners Required for Chemokine-directed T cell Migration

Stimulation of T cells leads to distinct changes of their adhesive and migratory properties. Signal propagation from activated receptors to integrins depends on scaffolding proteins such as the adhesion and degranulation promoting adaptor protein (ADAP)¹. Here we have comprehensively investigated the phosphotyrosine interactome of ADAP in T cells and define known and novel interaction partners of functional relevance. While most phosphosites reside in unstructured regions of the protein, thereby defining classical SH2 domain interaction sites for master regulators of T cell signaling such as SLP76, Fyn-kinase, and NCK, other binding events depend on structural context. Interaction proteomics using different ADAP constructs comprising most of the known phosphotyrosine motifs as well as the structured domains confirm that a distinct set of proteins is attracted by pY571 of ADAP, including the ζ-chain-associated protein kinase of 70 kDa (ZAP70). The interaction of ADAP and ZAP70 is inducible upon stimulation either of the T cell receptor (TCR) or by chemokine. NMR spectroscopy reveals that the N-terminal SH2 domains within a ZAP70-tandem-SH2 construct is the major site of interaction with phosphorylated ADAP-hSH3^N and microscale thermophoresis (MST) indicates an intermediate binding affinity (K_d = 2.3 μm). Interestingly, although T cell receptor dependent events such as T cell/antigen presenting cell (APC) conjugate formation and adhesion are not affected by mutation of Y571, migration of T cells along a chemokine gradient is compromised. Thus, although most phospho-sites in ADAP are linked to T cell receptor related functions we have identified a unique phosphotyrosine that is solely required for chemokine induced T cell behavior.T cell migration and the establishment of productive T cell/APC interactions are regulated by the activity of integrins. In resting T cells, integrins are expressed in an inactive state that adopts a conformation with low affinity for their ligands. Members of the intercellular adhesion molecule family (ICAM 1–5) are the physiological ligands of lymphocyte function-associated antigen 1 (LFA-1, αLβ2-integrin) whereas vascular cell adhesion molecule (VCAM) and fibronectin are the ligands for the β1-integrin very late antigen 4 (VLA-4) (1, 2). Triggering of the T cell receptor (TCR) by peptide-major histocompatibility complex (MHC) or stimulation of chemokine receptors (e.g. CCR7 with CCL21 or CXCR4 with CXCL12) induces a conformational change of the integrins that increases their ligand binding (affinity regulation) and subsequently mediates clustering of integrins at the cell surface (avidity regulation). The intracellular events leading to integrin activation have collectively been termed inside-out signaling. Conversely, ligand-bound integrins transmit a signal to the T cell and thereby promote adhesion, activation, proliferation, and migration of T cells (outside-in signaling) (1, 2).In both inside-out and outside-in signaling pathways tyrosine phosphorylation of adaptor proteins, either present as transmembrane scaffolds or as transiently membrane-anchored proteins, is a crucial primary event in signal transmission to integrins.An essential functional module operating at the integrin-membrane-cytoskeleton interface contains the cytosolic adaptor protein ADAP at its core. Ablation of ADAP in mice leads to dysfunctional integrin clustering and activity, thus compromising the adhesive and migratory properties of these cells. In addition to its instantaneous effects on cellular motility, ADAP was shown to act as a regulator of NFκB p65 nuclear translocation (3), a function that might well contribute to the observed modulation of cytokine production, like interleukin-2 (4, 5). A contribution of ADAP to mast cell degranulation has been postulated (6), and its complex formation with cytoskeletal regulators during early phases of phagocytosis in macrophages has been recognized early on (7). ADAP is also critical for normal platelet adhesion (8) and mutations in the human protein have recently been suggested to form an underlying genetic cause for autosomal recessive thrombocytopenia (9).ADAP interacts with several effectors of T cell function, either constitutively or phosphorylation-dependent. The SH3 domain of SKAP55 (Src-kinase associated phosphoprotein of 55 kDa) interacts with a proline-rich sequence (PRS) stretch in ADAP (Fig. 1A) (10, 11), whereas another PRS (FPPPP) is responsible for the interaction with the actin regulator Ena/VASP-like protein (EVL) (12). Membrane binding of the ADAP-SKAP55 complex is conferred by the PH domain of SKAP55 and to a lower extend by the C-terminal hSH3 domain (hSH3^C) of ADAP (13–16). Moreover, ADAP is strongly tyrosine-phosphorylated upon TCR stimulation and thereby serves as a hub for SH2 domain-containing proteins such as SLP76, FYN and NCK (Fig. 1A) (17–21). Beside these well characterized interactions, several other SH2-domain containing binders were identified by pull-down approaches using phosphorylated peptide baits (Fig. 1A) (22, 23). Most of the so far characterized SH2-pTyr interactions in ADAP are mapped to unstructured regions. An exception is Y571, which is located in close proximity to the folded hSH3^N domain of ADAP. Phosphoproteomic profiling of activated T cells has identified Y571 as a major phosphorylation site in ADAP (18, 24–30). Our rationale for the experimental approach chosen here was that the constraints imposed by the folding of the hSH3 domains impact the choice of SH2 domains that bind to such motifs in ADAP.Open in a separate windowFig. 1.Phosphotyrosine sites of ADAP and interaction partners. A, Schematic overview of the ADAP primary structure indicating interaction partners of different phosphotyrosine sites identified by peptide pull-down approaches (22, 23). Black arrows show SH2-pTyr interaction sites. White arrows show interactions dependent on proline rich sequences (PRS). B, Fyn kinase catalyzed in vitro phosphorylation of full-length ADAP. Identification and relative quantification of phosphorylation degrees of individual tyrosine residues was obtained by mass spectrometry. Phosphorylation degrees were estimated by comparing relative MS peak intensities of the corresponding peptide/phosphopeptide pairs as described (33, 34).To meet this challenge, we employed interaction proteomics and immunoprecipitation experiments using different constructs of ADAP that comprise the major phosphotyrosine sites including the two folded hSH3 domains. In particular, Y571, a residue residing at the domain border of the hSH3^N domain, is shown to interact with proteins that are not identified by the peptide pull-down approach. We identify the ZAP70 kinase as the most robust binding partner of pY571 and show that this interaction is maintained in primary T cells. Using NMR spectroscopy we further show that the N-terminal SH2 domain of ZAP70 is responsible for binding and we confirm the direct interaction between the two proteins to be inducible upon T cell receptor or CXCR4 stimulation. Abolishing the interaction by using a Y571F mutation compromises T cell migration along a CXCL12 gradient but does not affect TCR- and CXCR4-mediated adhesion and T cell interaction with APCs. In this way, the Y571F mutant of ADAP provides the striking example of a molecular switch that selectively invokes the migratory, but not the adhesive, signaling pathways in T cells.     

Sortase A mediated site‐specific immobilization for identification of protein interactions in affinity purification–mass spectrometry experiments

Proteomics approaches using MS in combination with affinity purification have emerged as powerful tools to study protein‐protein interactions. Here we make use of the specificity of sortase A transpeptidation reaction to prepare affinity matrices in which a protein bait is covalently linked to the matrix via a short C‐terminal linker region. As a result of this site‐directed immobilization, the bait remains functionally accessible to protein interactions. To apply this approach, we performed SILAC‐based pull‐down experiments and demonstrate the suitability of the approach.