Inside the “African Cattle Complex”: Animal Burials in the Holocene Central Sahara

Cattle pastoralism is an important trait of African cultures. Ethnographic studies describe the central role played by domestic cattle within many societies, highlighting its social and ideological value well beyond its mere function as ‘walking larder’. Historical depth of this African legacy has been repeatedly assessed in an archaeological perspective, mostly emphasizing a continental vision. Nevertheless, in-depth site-specific studies, with a few exceptions, are lacking. Despite the long tradition of a multi-disciplinary approach to the analysis of pastoral systems in Africa, rarely do early and middle Holocene archaeological contexts feature in the same area the combination of settlement, ceremonial and rock art features so as to be multi-dimensionally explored: the Messak plateau in the Libyan central Sahara represents an outstanding exception. Known for its rich Pleistocene occupation and abundant Holocene rock art, the region, through our research, has also shown to preserve the material evidence of a complex ritual dated to the Middle Pastoral (6080–5120 BP or 5200–3800 BC). This was centred on the frequent deposition in stone monuments of disarticulated animal remains, mostly cattle. Animal burials are known also from other African contexts, but regional extent of the phenomenon, state of preservation of monuments, and associated rock art make the Messak case unique. GIS analysis, excavation data, radiocarbon dating, zooarchaeological and isotopic (Sr, C, O) analyses of animal remains, and botanical information are used to explore this highly formalized ritual and the lifeways of a pastoral community in the Holocene Sahara.     

A population‐based temporal logic gate for timing and recording chemical events

Engineered bacterial sensors have potential applications in human health monitoring, environmental chemical detection, and materials biosynthesis. While such bacterial devices have long been engineered to differentiate between combinations of inputs, their potential to process signal timing and duration has been overlooked. In this work, we present a two‐input temporal logic gate that can sense and record the order of the inputs, the timing between inputs, and the duration of input pulses. Our temporal logic gate design relies on unidirectional DNA recombination mediated by bacteriophage integrases to detect and encode sequences of input events. For an E. coli strain engineered to contain our temporal logic gate, we compare predictions of Markov model simulations with laboratory measurements of final population distributions for both step and pulse inputs. Although single cells were engineered to have digital outputs, stochastic noise created heterogeneous single‐cell responses that translated into analog population responses. Furthermore, when single‐cell genetic states were aggregated into population‐level distributions, these distributions contained unique information not encoded in individual cells. Thus, final differentiated sub‐populations could be used to deduce order, timing, and duration of transient chemical events.     

An innovative approach for testing bioinformatics programs using metamorphic testing

Background  

Recent advances in experimental and computational technologies have fueled the development of many sophisticated bioinformatics programs. The correctness of such programs is crucial as incorrectly computed results may lead to wrong biological conclusion or misguide downstream experimentation. Common software testing procedures involve executing the target program with a set of test inputs and then verifying the correctness of the test outputs. However, due to the complexity of many bioinformatics programs, it is often difficult to verify the correctness of the test outputs. Therefore our ability to perform systematic software testing is greatly hindered.     

Structure of SP-B/DPPC mixed films studied by neutron reflectometry

The structures of films of pulmonary surfactant protein B (SP-B) and mixtures of SP-B and dipalmitoylphosphatidylcholine (DPPC) at the air/water interface have been studied by neutron reflectometry and Langmuir film balance methods. From the film balance studies, we observe that the isotherms of pure DPPC and SP-B/DPPC mixtures very nearly overlay one another at very high pressures, suggesting that the SP-B is being excluded from the film. The use of multiple contrasts with neutron reflectometry at a range of surface pressures has enabled the mixing and squeeze out of the DPPC and SP-B mixtures to be studied. We can identify the SP-B component of the interfacial structure and its position as a function of surface pressure. The mixtures are initially a homogeneous layer at low surface pressures. At higher surface pressures, the SP-B is squeezed out of the lipid layer into the subphase, with the first signs detected at 30 mN m⁻¹. At 50 mN m⁻¹, the subphase is almost completely excluded from the DPPC layer, with the SP-B content significantly reduced. Only a small amount of DPPC appears to be associated with the squeezed out SP-B.     

A genetic ensemble approach for gene-gene interaction identification

Background  

It has now become clear that gene-gene interactions and gene-environment interactions are ubiquitous and fundamental mechanisms for the development of complex diseases. Though a considerable effort has been put into developing statistical models and algorithmic strategies for identifying such interactions, the accurate identification of those genetic interactions has been proven to be very challenging.