Mechanism of homology recognition in DNA recombination from dual-molecule experiments

In E. coli homologous recombination, a filament of RecA protein formed on DNA searches and pairs a homologous sequence within a second DNA molecule with remarkable speed and fidelity. Here, we directly probe the strength of the two-molecule interactions involved in homology search and recognition using dual-molecule manipulation, combining magnetic and optical tweezers. We find that the filament's secondary DNA-binding site interacts with a single strand of the incoming double-stranded DNA during homology sampling. Recognition requires opening of the helix and is strongly promoted by unwinding torsional stress. Recognition is achieved upon binding of both strands of the incoming dsDNA to each of two ssDNA-binding sites in the filament. The data indicate a physical picture for homology recognition in which the fidelity of the search process is governed by the distance between the DNA-binding sites.     

Marine ostracod provinciality in the late ordovician of palaeocontinental laurentia and its environmental and geographical expression

Background

We examine the environmental, climatic and geographical controls on tropical ostracod distribution in the marine Ordovician of North America.

Methodology/Principal Findings

Analysis of the inter-regional distribution patterns of Ordovician Laurentian ostracods, focussing particularly on the diverse Late Ordovician Sandbian (ca 461 to 456 Ma) faunas, demonstrates strong endemicity at the species-level. Local endemism is very pronounced, ranging from 25% (e.g. Foxe basin) to 75% (e.g. Michigan basin) in each basin, a pattern that is also reflected in other benthic faunas such as brachiopods. Multivariate (ordination) analyses of the ostracod faunas allow demarcation of a Midcontinent Province and a southern Marginal Province in Laurentia. While these are most clearly differentiated at the stratigraphical level of the bicornis graptolite biozone, analyses of the entire dataset suggest that these provinces remain distinct throughout the Sandbian interval. Differences in species composition between the provinces appear to have been controlled by changes in physical parameters (e.g. temperature and salinity) related to water depth and latitude and a possible regional geographic barrier, and these differences persist into the Katian and possibly the Hirnantian. Local environmental parameters, perhaps operating at the microhabitat scale, may have been significant in driving local speciation events from ancestor species in each region.

Conclusions/Significance

Our work establishes a refined methodology for assessing marine benthic arthropod micro-benthos provinciality for the Early Palaeozoic.     

Novel role for galectin-8 protein as mediator of coagulation factor V endocytosis by megakaryocytes

Galectin-8 (Gal8) interacts with β-galactoside-containing glycoproteins and has recently been implicated to play a role in platelet activation. It has been suggested that Gal8 may also interact with platelet coagulation factor V (FV). This indispensable cofactor is stored in α-granules of platelets via a poorly understood endocytic mechanism that only exists in megakaryocytes (platelet precursor cells). In this study, we now assessed the putative role of Gal8 for FV biology. Surface plasmon resonance analysis and a solid phase binding assay revealed that Gal8 binds FV. The data further show that β-galactosides block the interaction between FV and Gal8. These findings indicate that Gal8 specifically interacts with FV in a carbohydrate-dependent manner. Confocal microscopy studies and flow cytometry analysis demonstrated that megakaryocytic DAMI cells internalize FV. Flow cytometry showed that these cells express Gal8 on their cell surface. Reducing the functional presence of Gal8 on the cells either by an anti-Gal8 antibody or by siRNA technology markedly impaired the endocytic uptake of FV. Compatible with the apparent role of Gal8 for FV uptake, endocytosis of FV was also affected in the presence of β-galactosides. Strikingly, thrombopoietin-differentiated DAMI cells, which represent a more mature megakaryocytic state, not only lose the capacity to express cell-surface bound Gal8 but also lose the ability to internalize FV. Collectively, our data reveal a novel role for the tandem repeat Gal8 in promoting FV endocytosis.     

Comparing Inductive and Deductive Modeling of Land Use Decisions: Principles,a Model and an Illustration from the Philippines

Understanding the causes of land use change is of great importance for issues of tropical deforestation, agricultural development and biodiversity conservation. Many quantitative studies, therefore, aim to link land use change to its causal ‘driving forces.’ The epistemology of virtually all these studies is inductive, searching for correlations within relatively large, sometimes spatially explicit, datasets. This can be sound science but we here aim to exemplify that there is also scope for more deductive approaches that test a pre-defined explanatory theory. The paper first introduces the principles and merits of inductive and more deductive types of land use modeling. It then presents one integrated causal model that is subsequently specified to predict land use in an area in northeastern Philippines in a deductive manner, and tested against the observed land use in that area. The same set of land use data is also used in an inductive (multinomial regression) approach. With a goodness-of-prediction of 70% of the deductive model and a goodness-of-fit of 77% of the inductive model, both perform equally well, statistically. Because the deductive model explicitly contains not only the causal factors but also the causal mechanisms that explain land use, the deductive model then provides a more truly causal, as well as more theory-connected, understanding of land use. This provides land use scholarship with an invitation to add more deductive (theory-driven and theory-building) daring to its methodological repertoire.

Archaeological charcoals as archives for firewood preferences and vegetation composition during the late Holocene in the southern Mayumbe,Democratic Republic of the Congo (DRC)

Analysis of charcoal from an archaeological assemblage near the Lukula community located at the southernmost boundary of the Mayombe forest (Bas-Congo, DRC) yielded 30 taxa used as firewood between 1,200 and 700 cal. b.p. Local people mentioned 71 taxa preferred for use nowadays. The identified taxa belong either to mature rainforest, pioneer forest, regenerating forest or woodland savanna, indicating that ancient and current local populations gathered firewood in several different forest types. Modern firewood preferences do not seem to agree with the archaeobotanical composition. Also, linguistic evidence does not indicate a long exploitation history for all of the recorded taxa. Furthermore, no particular wood qualities such as wood density, calorific value or magical or medicinal properties seem to determine the Lukula assemblage, which was probably composed of waste material from various activities which required different specific firewood characteristics. As such, taxa composition is not biased by human selection, suggesting that it reflects the surrounding environment, which was characterised by mature rainforest with patches of regenerating forest and open vegetation types. Unlike the origin of present-day forest-savanna mosaics from human activity, fragmentation around 1,000 cal. b.p. may have been provoked by a well-known climatic event coinciding with the Medieval Climate Anomaly, which undoubtedly had a significant impact on Central African forest composition.     

Optic Nerve Sheath Diameter Remains Constant during Robot Assisted Laparoscopic Radical Prostatectomy

Background

During robot assisted laparoscopic radical prostatectomy (RALRP), a CO₂ pneumoperitoneum (CO₂PP) is applied and the patient is placed in a head-down position. Intracranial pressure (ICP) is expected to acutely increase under these conditions. A non-invasive method, the optic nerve sheath diameter (ONSD) measurement, may warn us that the mechanism of protective cerebrospinal fluid (CSF) shifts becomes exhausted.

Methods

After obtaining IRB approval and written informed consent, ONSD was measured by ocular ultrasound in 20 ASA I–II patients at various stages of the RALRP procedure: baseline awake, after induction, after applying the CO₂PP, during head-down position, after resuming the supine position, in the postoperative anaesthesia care unit, and on day one postoperatively. Cerebral perfusion pressure (CPP) was calculated as the mean arterial (MAP) minus central venous pressure (CVP).

Results

The ONSD did not change during head-down position, although the CVP increased from 4.2(2.5) mm Hg to 27.6(3.8) mm Hg. The CPP was decreased 70 min after assuming the head-down position until 15 min after resuming the supine position, but remained above 60 mm Hg at all times.

Conclusion

Even though ICP has been documented to increase during CO₂PP and head-down positioning, we did not find any changes in ONSD during head-down position. These results indicate that intracranial blood volume does not increase up to a point that CSF migration as a compensation mechanism becomes exhausted, suggesting any increases in ICP are likely to be small.     

Role of energy systems in two intermittent field tests in women field hockey players

The energetics of 2 field tests that reflect physical performance in intermittent sports (i.e., the Interval Shuttle Sprint Test [ISST] and the Interval Shuttle Run Test [ISRT]) were examined in 21 women field hockey players. The ISST required the players to perform 10 shuttle sprints starting every 20 seconds. During the ISRT, players alternately ran 20-m shuttles for 30 seconds and walked for 15 seconds with increasing speed. Anaerobic and aerobic power tests included Wingate cycle sprints and a .V(O2)max cycle test, respectively. Based on correlation and regression analyses, it was concluded that for the ISST, anaerobic energetic pathways contribute mainly to energy supply for peak sprint time, while aerobic energetic pathways also contribute to energy supply for total sprint time. Energy during the ISRT is supplied mainly by the aerobic energy system. Depending on the aspect of physical performance a coach wants to determine, the ISST or ISRT can be used.