Detection and characterization of local inverted repeats regularities

To explore the inverted repeats regularities along the genome sequences, we propose a sliding window method to extract the concentration scores of inverted repeats periodic regularities and the total mass of possible inverted repeats pairs. We apply the method to the human genome and locate the regions with the potential for the formation of large number of hairpin/cruciform structures. The number of found windows with periodic regularities is small and the patterns of occurrence are chromosome specific.publishe

Faster subsequence recognition in compressed strings

Computation on compressed strings is one of the key approaches to processing massive data sets. We consider local subsequence recognition problems on strings compressed by straight-line programs (SLP), which is closely related to Lempel--Ziv compression. For an SLP-compressed text of length $\bar m$, and an uncompressed pattern of length $n$, C{\'e}gielski et al. gave an algorithm for local subsequence recognition running in time $O(\bar mn^2 \log n)$. We improve the running time to $O(\bar mn^{1.5})$. Our algorithm can also be used to compute the longest common subsequence between a compressed text and an uncompressed pattern in time $O(\bar mn^{1.5})$; the same problem with a compressed pattern is known to be NP-hard

Biogeographical survey of soil microbiomes across sub-Saharan Africa:structure, drivers, and predicted climate-driven changes

BACKGROUND: Top-soil microbiomes make a vital contribution to the Earth’s ecology and harbor an extraordinarily high biodiversity. They are also key players in many ecosystem services, particularly in arid regions of the globe such as the African continent. While several recent studies have documented patterns in global soil microbial ecology, these are largely biased towards widely studied regions and rely on models to interpolate the microbial diversity of other regions where there is low data coverage. This is the case for sub-Saharan Africa, where the number of regional microbial studies is very low in comparison to other continents. RESULTS: The aim of this study was to conduct an extensive biogeographical survey of sub-Saharan Africa’s top-soil microbiomes, with a specific focus on investigating the environmental drivers of microbial ecology across the region. In this study, we sampled 810 sample sites across 9 sub-Saharan African countries and used taxonomic barcoding to profile the microbial ecology of these regions. Our results showed that the sub-Saharan nations included in the study harbor qualitatively distinguishable soil microbiomes. In addition, using soil chemistry and climatic data extracted from the same sites, we demonstrated that the top-soil microbiome is shaped by a broad range of environmental factors, most notably pH, precipitation, and temperature. Through the use of structural equation modeling, we also developed a model to predict how soil microbial biodiversity in sub-Saharan Africa might be affected by future climate change scenarios. This model predicted that the soil microbial biodiversity of countries such as Kenya will be negatively affected by increased temperatures and decreased precipitation, while the fungal biodiversity of Benin will benefit from the increase in annual precipitation. CONCLUSION: This study represents the most extensive biogeographical survey of sub-Saharan top-soil microbiomes to date. Importantly, this study has allowed us to identify countries in sub-Saharan Africa that might be particularly vulnerable to losses in soil microbial ecology and productivity due to climate change. Considering the reliance of many economies in the region on rain-fed agriculture, this study provides crucial information to support conservation efforts in the countries that will be most heavily impacted by climate change. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40168-022-01297-w

Drivers for international innovation activities in developed and emerging countries

This paper aims to shed light on firm specific drivers that lead firms to internationalise their innovation activities. The paper draws a comprehensive picture of driving forces by including firm capabilities, characteristics of the firm’s competitive environment and the influence of innovation obstacles in the home country. In particular, the role of the potential driving forces is tested on the probability to carry out different innovative activities abroad (R&D, design/conception of new products, manufacturing of innovative products and implementation of new processes). In a second step these driving forces are used to observe their impact on the decision to locate innovation activities in various countries and regions (China, Eastern Europe, Western Europe and North America) as well as in groups of countries with similar levels of knowledge (country clubs). The analysis is based on the Mannheim Innovation Panel survey which represents the German CIS (Community Innovation Survey) contribution. Two survey waves are combined and result in a sample of about 1400 firms. The results show that the decision to perform innovation activities abroad is mainly driven by organisational capabilities such as absorptive capacities, international experience and existing technological competences of the respective firm. Innovation barriers at the German home base such as lack of labour and high innovation costs foster the set up of later-stage innovation activities abroad while the lack of demand demonstrates a barrier to the internationalisation decision for the development and manufacturing of new products. Location decisions receive the strongest influencing effects from the international experience of the firm. Firms which innovate in developing countries seem to require a more extensive level of international experience by international R&D cooperation

How contemporary bioclimatic and human controls change global fire regimes

Anthropogenically driven declines in tropical savannah burnt area have recently received attention due to their effect on trends in global burnt area. Large-scale trends in ecosystems where vegetation has adapted to infrequent fire, especially in cooler and wetter forested areas, are less well understood. Here, small changes in fire regimes can have a substantial impact on local biogeochemistry. To investigate trends in fire across a wide range of ecosystems, we used Bayesian inference to quantify four primary controls on burnt area: fuel continuity, fuel moisture, ignitions and anthropogenic suppression. We found that fuel continuity and moisture are the dominant limiting factors of burnt area globally. Suppression is most important in cropland areas, whereas savannahs and boreal forests are most sensitive to ignitions. We quantify fire regime shifts in areas with more than one, and often counteracting, trends in these controls. Forests are of particular concern, where we show average shifts in controls of 2.3–2.6% of their potential maximum per year, mainly driven by trends in fuel continuity and moisture. This study gives added importance to understanding long-term future changes in the controls on fire and the effect of fire trends on ecosystem function

The importance of interacting climate modes on Australia’s contribution to global carbon cycle extremes

The global carbon cycle is highly sensitive to climate-driven fluctuations of precipitation, especially in the Southern Hemisphere. This was clearly manifested by a 20% increase of the global terrestrial C sink in 2011 during the strongest sustained La Niña since 1917. However, inconsistencies exist between El Niño/La Niña (ENSO) cycles and precipitation in the historical record; for example, significant ENSO-precipitation correlations were present in only 31% of the last 100 years, and often absent in wet years. To resolve these inconsistencies, we used an advanced temporal scaling method for identifying interactions amongst three key climate modes (El Niño, the Indian Ocean dipole, and the southern annular mode). When these climate modes synchronised (1999-2012), drought and extreme precipitation were observed across Australia. The interaction amongst these climate modes, more than the effect of any single mode, was associated with large fluctuations in precipitation and productivity. The long-term exposure of vegetation to this arid environment has favoured a resilient flora capable of large fluctuations in photosynthetic productivity and explains why Australia was a major contributor not only to the 2011 global C sink anomaly but also to global reductions in photosynthetic C uptake during the previous decade of drought

Fire History from Life-History: Determining the Fire Regime that a Plant Community Is Adapted Using Life-Histories

Wildfire is a fundamental disturbance process in many ecological communities, and is critical in maintaining the structure of some plant communities. In the past century, changes in global land use practices have led to changes in fire regimes that have radically altered the composition of many plant communities. As the severe biodiversity impacts of inappropriate fire management regimes are recognized, attempts are being made to manage fires within a more ‘natural’ regime. In this aim, the focus has typically been on determining the fire regime to which the community has adapted. Here we take a subtly different approach and focus on the probability of a patch being burnt. We hypothesize that competing sympatric taxa from different plant functional groups are able to coexist due to the stochasticity of the fire regime, which creates opportunities in both time and space that are exploited differentially by each group. We exploit this situation to find the fire probability at which three sympatric grasses, from different functional groups, are able to co-exist. We do this by parameterizing a spatio-temporal simulation model with the life-history strategies of the three species and then search for the fire frequency and scale at which they are able to coexist when in competition. The simulation gives a clear result that these species only coexist across a very narrow range of fire probabilities centred at 0.2. Conversely, fire scale was found only to be important at very large scales. Our work demonstrates the efficacy of using competing sympatric species with different regeneration niches to determine the probability of fire in any given patch. Estimating this probability allows us to construct an expected historical distribution of fire return intervals for the community; a critical resource for managing fire-driven biodiversity in the face of a growing carbon economy and ongoing climate change

Assay platform for clinically relevant metallo-beta-lactamases

Metallo-β-lactamases (MBLs) are a growing threat to the use of almost all clinically used β-lactam antibiotics. The identification of broad-spectrum MBL inhibitors is hampered by the lack of a suitable screening platform, consisting of appropriate substrates and a set of clinically relevant MBLs. We report procedures for the preparation of a set of clinically relevant metallo-β-lactamases (i.e., NDM-1 (New Delhi MBL), IMP-1 (Imipenemase), SPM-1 (São Paulo MBL), and VIM-2 (Verona integron-encoded MBL)) and the identification of suitable fluorogenic substrates (umbelliferone-derived cephalosporins). The fluorogenic substrates were compared to chromogenic substrates (CENTA, nitrocefin, and imipenem), showing improved sensitivity and kinetic parameters. The efficiency of the fluorogenic substrates was exemplified by inhibitor screening, identifying 4-chloroisoquinolinols as potential pan MBL inhibitors

Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae)

Background: Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse nature, importance as pollinators, and historical instability with regard to subfamilial and tribal classification, Syrphidae (flower flies or hoverflies) are an ideal candidate for anchored hybrid enrichment-based phylogenetics, especially since recent molecular phylogenies of the syrphids using only a few markers have resulted in highly unresolved topologies. Over 6200 syrphids are currently known and uncovering their phylogeny will help us to understand how these species have diversified, providing insight into an array of ecological processes, from the development of adult mimicry, the origin of adult migration, to pollination patterns and the evolution of larval resource utilization. Results: We present the first use of anchored hybrid enrichment in insect phylogenetics on a dataset containing 30 flower fly species from across all four subfamilies and 11 tribes out of 15. To produce a phylogenetic hypothesis, 559 loci were sampled to produce a final dataset containing 217,702 sites. We recovered a well resolved topology with bootstrap support values that were almost universally >95 %. The subfamily Eristalinae is recovered as paraphyletic, with the strongest support for this hypothesis to date. The ant predators in the Microdontinae are sister to all other syrphids. Syrphinae and Pipizinae are monophyletic and sister to each other. Larval predation on soft-bodied hemipterans evolved only once in this family. Conclusions: Anchored hybrid enrichment was successful in producing a robustly supported phylogenetic hypothesis for the syrphids. Subfamilial reconstruction is concordant with recent phylogenetic hypotheses, but with much higher support values. With the newly designed probe kit this analysis could be rapidly expanded with further sampling, opening the door to more comprehensive analyses targeting problem areas in syrphid phylogenetics and ecology.Peer reviewe