From Simple Bacterial and Archaeal Replicons to Replication N/U-Domains

The Replicon Theory proposed 50 years ago has proven to apply for replicons of the three domains of life. Here, we review our knowledge of genome organization into single and multiple replicons in bacteria, archaea and eukarya. Bacterial and archaeal replicator/initiator systems are quite specific and efficient, whereas eukaryotic replicons show degenerate specificity and efficiency, allowing for complex regulation of origin firing time. We expand on recent evidence that ~ 50% of the human genome is organized as ~ 1,500 megabase-sized replication domains with a characteristic parabolic (U-shaped) replication timing profile and linear (N-shaped) gradient of replication fork polarity. These N/U-domains correspond to self-interacting segments of the chromatin fiber bordered by open chromatin zones and replicate by cascades of origin firing initiating at their borders and propagating to their center, possibly by fork-stimulated initiation. The conserved occurrence of this replication pattern in the germline of mammals has resulted over evolutionary times in the formation of megabase-sized domains with an N-shaped nucleotide compositional skew profile due to replication-associated mutational asymmetries. Overall, these results reveal an evolutionarily conserved but developmentally plastic organization of replication that is driving mammalian genome evolution.     

The first lace bug from Chiapas amber (Totolapa,Mexico) (Hemiptera: Tingidae)

Leptopharsa tacanae sp. nov., the first Tingidae from Mexican amber, is described and its morphological affinities are discussed.     

Phenotypic plasticity in evolutionary rescue experiments

Population persistence in a new and stressful environment can be influenced by the plastic phenotypic responses of individuals to this environment, and by the genetic evolution of plasticity itself. This process has recently been investigated theoretically, but testing the quantitative predictions in the wild is challenging because (i) there are usually not enough population replicates to deal with the stochasticity of the evolutionary process, (ii) environmental conditions are not controlled, and (iii) measuring selection and the inheritance of traits affecting fitness is difficult in natural populations. As an alternative, predictions from theory can be tested in the laboratory with controlled experiments. To illustrate the feasibility of this approach, we briefly review the literature on the experimental evolution of plasticity, and on evolutionary rescue in the laboratory, paying particular attention to differences and similarities between microbes and multicellular eukaryotes. We then highlight a set of questions that could be addressed using this framework, which would enable testing the robustness of theoretical predictions, and provide new insights into areas that have received little theoretical attention to date.     

A comparative analysis of metabarcoding and morphology‐based identification of benthic communities across different regional seas

In a world of declining biodiversity, monitoring is becoming crucial. Molecular methods, such as metabarcoding, have the potential to rapidly expand our knowledge of biodiversity, supporting assessment, management, and conservation. In the marine environment, where hard substrata are more difficult to access than soft bottoms for quantitative ecological studies, Artificial Substrate Units (ASUs) allow for standardized sampling. We deployed ASUs within five regional seas (Baltic Sea, Northeast Atlantic Ocean, Mediterranean Sea, Black Sea, and Red Sea) for 12–26 months to measure the diversity and community composition of macroinvertebrates. We identified invertebrates using a traditional approach based on morphological characters, and by metabarcoding of the mitochondrial cytochrome oxidase I (COI) gene. We compared community composition and diversity metrics obtained using the two methods. Diversity was significantly correlated between data types. Metabarcoding of ASUs allowed for robust comparisons of community composition and diversity, but not all groups were successfully sequenced. All locations were significantly different in taxonomic composition as measured with both kinds of data. We recovered previously known regional biogeographical patterns in both datasets (e.g., low species diversity in the Black and Baltic Seas, affinity between the Bay of Biscay and the Mediterranean). We conclude that the two approaches provide complementary information and that metabarcoding shows great promise for marine monitoring. However, until its pitfalls are addressed, the use of metabarcoding in monitoring of rocky benthic assemblages should be used in addition to classical approaches rather than instead of them.     

The persistent decline of patterned woody vegetation: The tiger bush in the context of the regional Sahel greening trend

Following 25 years of below average annual rainfall in the Sahel between 1970 and 1995, the return to more humid conditions has led to rapid postdrought recovery of the woody cover. However, the increase in the woody cover is not spatially homogeneous raising questions about the resilience of some woody vegetation types. Based on the analysis of field and remote sensing data collected on the tiger bush systems in the northern Sahel in Mali, this study noted the current and persistent degradation of these systems in the Sahel since the 1970s despite the recent improvement in rainfall since the mid‐1990s and the general Sahel re‐greening. Profound changes in the woody population pattern, tree density and cover, and floristic composition took place regardless of the site location along the south–north rainfall gradient. Associated with definite structural changes of the woody population, surface hydrology shifted from a sheet to concentrated run‐off accelerating the collapse of the patterned woody population. Currently, there is no evidence in favour of reversing the current degradation process, at least at a decadal scale, although very sparse recolonization by pioneer woody vegetation has been observed in the driest sites along recently formed gullies. These observations support the hypothesis of an ecosystem shift, with long‐term implications for the structure and functioning of the patterned vegetation, as well as the whole watershed landscape through increased run‐off leading to stronger water flows in enlarged wadis, increased soil erosion upstream and sediment deposition downstream, enhanced water storage in ponds, and greater recharge of aquifers, which is an illustration of the “Sahelian paradox”.     

A trade-based method for modelling supply markets in consequential LCA exemplified with Portland cement and bananas

Purpose

This study proposes a method based on the analysis of trade networks over time for modelling the marginal supply of products in consequential life cycle assessment (LCA). It aims at increasing the geographical granularity of markets, accuracy of transport distances and modes and material losses during transit by creating country-specific markets, instead of region-based supply-origin markets as currently proposed by ecoinvent. It leads to a better consideration of the environmental weight of trade following a change in demand on a local market and may serve as an inspirational basis for future releases of consequential life cycle inventory (LCI) databases.

Methods

The method uses ecoinvent v.3.3 as a support LCI database and two distinct traded products: bananas and grey Portland cement. Each country involved in the trade of a said product has a corresponding market created in the LCI database. The behavior of market to a marginal change in internal demand is modelled after its marginal trading preferences: it can either affect local production, imports, exports or a mix of the first two. Markets are linked to one another based on the linear regression analysis of their historical trade relations. The inventories that follow an increase in demand of 1000 kg of bananas and grey Portland cement are calculated for each market involved in their trade and are environmentally characterized and compared to the generic region-based market datasets provided by ecoinvent to assess the gains in accuracy through a higher geographical granularity. Furthermore, the characterized inventories of the markets for bananas are compared to a parallel scenario where transport distances are kept to a minimum using the shortest path method. It isolates the environmental burden associated to the utility maximization of the demand.

Results and discussion

When comparing the characterized impacts of country-specific markets with the generic ecoinvent market datasets, disparities in results appear. They highlight the importance of transport induced by demand displacement and losses of material during transport, both being the consequences of the extent a given market decides to be supplied directly from producing markets at the margin. These are aspects that may go unaccounted for when using generic regional markets. Second, optimizing transport distances for each market decreases the environmental impacts for most categories by more than 70%.

Conclusions

This study shows there is a need for modelling and understanding market relations to more accurately define the role of trade, supply chain efficiency and import policies in LCA.

     

An aminoacylase activity from Streptomyces ambofaciens catalyzes the acylation of lysine on α‐position and peptides on N‐terminal position

The presence of aminoacylase activities was investigated in a crude extract of Streptomyces ambofaciens ATCC23877. First activities catalyzing the hydrolysis of N‐α or ε‐acetyl‐L‐lysine were identified. Furthermore, the acylation of lysine and different peptides was studied and compared with results obtained with lipase B of Candida antarctica (CALB). Different regioselectivities were demonstrated for the two classes of enzymes. CALB was able to catalyze acylation only on the ε‐position whereas the crude extract from S. ambofaciens possessed the rare ability to catalyze the N‐acylation on the α‐position of the lysine or of the amino‐acid in N‐terminal position of peptides. Two genes, SAM23877_1485 and SAM23877_1734, were identified in the genome of Streptomyces ambofaciens ATCC23877 whose products show similarities with the previously identified aminoacylases from Streptomyces mobaraensis. The proteins encoded by these two genes were responsible for the major aminoacylase hydrolytic activities. Furthermore, we show that the hydrolysis of N‐α‐acetyl‐L‐lysine could be attributed to the product of SAM23877_1734 gene.     

West African Cattle Farmers’ Perception of Tick-Borne Diseases

Worldwide, cattle production is struggling to face the negative impacts caused by ticks and Rhipicephalus (Boophilus) microplus is one of the most harmful ticks for livestock. Most of the people in West Africa depend on cattle farming and subsistence agriculture. The presence of ticks on cattle is a major problem faced by smallholder farmers who fight for their livelihood. National and regional tick control programs could assist these rural communities in protecting their livelihoods against ticks and tick-borne diseases, but only if they take into account the targeted herders and their perception on cattle management and tick control. This paper aims to provide a better insight in the socio-economic characteristics of Beninese cattle farmers, and their perception on tick burden, as well as to document common tick control strategies. Different tick species and their seasonality are well understood by cattle herders. For tick control, many still use manual tick removal, especially in the north of the country. The high cost of acaricides, the lack of financial means of African farmers, and of the local stockbreeders in particular, limits the use of acaricides in livestock breeding in Benin. While aiming to increase the meat or milk production of their animals, stockbreeders who can afford it sometimes turn to an abusive use of acaricides, which might in time lead to an increase in tick resistance. This study remains one of the rare studies to report extensively on the perceptions of West African cattle herders.     

Novel bicyclic oxazolone derivatives as anti-angiogenic agents

Novel bicyclic tetrahydropyrano[3,2-d]oxazolones derivatives, analogues of Fumagillin, were synthesised via a stereocontrolled oxidative-rearrangement of furylcarbinols and subsequent treatment with the appropriate isocyanate. These compounds demonstrated potent antiangiogenic activity.