Rapid Evolution of Recombinant Saccharomyces cerevisiae for Xylose Fermentation through Formation of Extra-chromosomal Circular DNA

Circular DNA elements are involved in genome plasticity, particularly of tandem repeats. However, amplifications of DNA segments in Saccharomyces cerevisiae reported so far involve pre-existing repetitive sequences such as ribosomal DNA, Ty elements and Long Terminal Repeats (LTRs). Here, we report the generation of an eccDNA, (extrachromosomal circular DNA element) in a region without any repetitive sequences during an adaptive evolution experiment. We performed whole genome sequence comparison between an efficient D-xylose fermenting yeast strain developed by metabolic and evolutionary engineering, and its parent industrial strain. We found that the heterologous gene XylA that had been inserted close to an ARS sequence in the parent strain has been amplified about 9 fold in both alleles of the chromosomal locus of the evolved strain compared to its parent. Analysis of the amplification process during the adaptive evolution revealed formation of a XylA-carrying eccDNA, pXI2-6, followed by chromosomal integration in tandem arrays over the course of the evolutionary adaptation. Formation of the eccDNA occurred in the absence of any repetitive DNA elements, probably using a micro-homology sequence of 8 nucleotides flanking the amplified sequence. We isolated the pXI2-6 eccDNA from an intermediate strain of the evolutionary adaptation process, sequenced it completely and showed that it confers high xylose fermentation capacity when it is transferred to a new strain. In this way, we have provided clear evidence that gene amplification can occur through generation of eccDNA without the presence of flanking repetitive sequences and can serve as a rapid means of adaptation to selection pressure.     

African wolf diet,predation on livestock and conflict in the Guassa mountains of Ethiopia

The African wolf (Canis lupus lupaster) was first identified in 2011 in the Ethiopian highlands, with its status as a new species confirmed in 2015. We studied the diet of a confirmed African wolf population in the Menz‐Guassa Community Conservation Area of central Ethiopia from scat samples collected by den sites from August to November 2010. Rodents were found to be the principal food items occurring in 88.1% of scats (n = 101), followed by plant material (34.7%) and insects (21.8%). Information on reported livestock predation and ensuing conflict with the agro‐pastoral community was obtained through a questionnaire survey. Interview respondents listed the African wolf as the most serious predator of livestock, accounting for 74.6% of the reported kills (n = 492) and 78.9% of the economic loss. Over 70% of reported livestock predation occurred during the dry season (January–April). Better livestock management during this period may significantly reduce conflict. As sympatric Ethiopian wolves primarily feed on rodents, further studies on the foraging ecology, niche overlap and interspecific interactions between the two species should be studied to determine the extent of competition between the two species.     

Use of Occult Blood Detection Cards for Real-Time PCR-Based Diagnosis of Schistosoma Mansoni Infection

Background

In Schistosoma mansoni infection, diagnosis and control after treatment mainly rely on parasitological stool investigations which are laborious and have limited sensitivity. PCR methods have shown equal or superior sensitivity but preservation and storage methods limit their use in the field. Therefore, the use of occult blood detection cards (fecal cards) for easy sampling and storage of fecal samples for further PCR testing was evaluated in a pilot study.

Methodology

Stool specimens were collected in a highly endemic area for S. mansoni in Ethiopia and submitted in an investigator-blinded fashion to microscopic examination by Kato-Katz thick smear as well as to real-time PCR using either fresh frozen stool samples or stool smears on fecal cards which have been stored at ambient temperature for up to ten months.

Principal Findings

Out of 55 stool samples, 35 were positive by microscopy, 33 and 32 were positive by PCR of frozen samples and of fecal card samples, respectively. When microscopy was used as diagnostic “gold standard”, the sensitivity of PCR on fresh stool was 94.3% (95%-CI: 86.6; 100) and on fecal cards 91.4% (95%-CI: 82.2; 100).

Conclusions

The use of fecal cards proved to be a simple and useful method for stool collection and prolonged storage prior to PCR based diagnosis of S. mansoni infection. This technique may be a valuable approach for large scale surveillance and post treatment assessments     

Population size and habitat preference of the Omo River guereza (Colobus guereza guereza) in a multi-habitat matrix in the central highlands of Ethiopia

Primates - Given the current rate of habitat degradation and loss in the tropics, data on primate population densities and habitat use are indispensable for assessing conservation status and...     

Newly discovered Bale monkey populations in forest fragments in southern Ethiopia: evidence of crop raiding, hybridization with grivets, and other conservation threats

Until recently, the Bale monkey (Chlorocebus djamdjamensis), an arboreal primate endemic to the southern Ethiopian highlands, remained virtually unstudied, and its distribution pattern inadequately documented. To broaden our knowledge of the species' distribution and abundance, we carried out interviews with local people and total count surveys for Bale monkeys across 67 fragmented forest sites in human-dominated landscapes in the Oromia and Southern Nations, Nationalities, and People's Regions, Ethiopia. From January 2010 to May 2011, we discovered 26 new Bale monkey populations inhabiting forest fragments at elevations ranging from 2,355 to 3,204 m asl. Across these populations, we recorded 37 groups ranging in size from 9 to 29 individuals (Mean = 19.5, SD = 4.5), for a total of 722 individuals. Black-and-white colobus monkeys (Colobus guereza) were sympatric with Bale monkeys at all sites, while grivet monkeys (Chlorocebus aethiops) were found only at sites where Bale monkeys did not occur. All of the newly discovered Bale monkey sites once contained bamboo forest, though at 35% of the sites bamboo forest had been eliminated during the past two decades. The persistence of Bale monkeys at fragmented sites lacking bamboo suggests greater habitat flexibility for the species than previously thought, though the long-term viability of populations both with and without bamboo remains uncertain. Human hunting in response to crop raiding, a behavior the monkeys engaged in at all sites, represents a major threat facing the newly discovered Bale monkey populations. Furthermore, despite their current lack of sympatry, apparently hybrid individuals between Bale monkeys and grivets were noted at three sites, posing yet another potential obstacle to Bale monkey conservation. Community conservation programs aimed at (1) protecting remaining habitat fragments, (2) planting bamboo and trees within and between fragments, and (3) reducing crop raiding represent the only hope for survival of the newly discovered Bale monkey populations.     

Enhanced succinic acid production under acidic conditions by introduction of glutamate decarboxylase system in E. coli AFP111

Bioprocess and Biosystems Engineering - Biological synthesis of succinic acid at low pH values was favored since it not only decreased investment cost but also simplified downstream purification...