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Duplication and deletion of the 1.4-Mb region in 17p12 that is delimited by two 24-kb low copy number repeats (CMT1A-REPs) represent frequent genomic rearrangements resulting in two common inherited peripheral neuropathies, Charcot-Marie-Tooth disease type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsy (HNPP). CMT1A and HNPP exemplify a paradigm for genomic disorders wherein unique genome architectural features result in susceptibility to DNA rearrangements that cause disease. A gene within the 1.4-Mb region, PMP22, is responsible for these disorders through a gene-dosage effect in the heterozygous duplication or deletion. However, the genomic structure of the 1.4-Mb region, including other genes contained within the rearranged genomic segment, remains essentially uncharacterized. To delineate genomic structural features, investigate higher-order genomic architecture, and identify genes in this region, we constructed PAC and BAC contigs and determined the complete nucleotide sequence. This CMT1A/HNPP genomic segment contains 1,421,129 bp of DNA. A low copy number repeat (LCR) was identified, with one copy inside and two copies outside of the 1.4-Mb region. Comparison between physical and genetic maps revealed a striking difference in recombination rates between the sexes with a lower recombination frequency in males (0.67 cM/Mb) versus females (5.5 cM/Mb). Hypothetically, this low recombination frequency in males may enable a chromosomal misalignment at proximal and distal CMT1A-REPs and promote unequal crossing over, which occurs 10 times more frequently in male meiosis. In addition to three previously described genes, five new genes (TEKT3, HS3ST3B1, NPD008/CGI-148, CDRT1, and CDRT15) and 13 predicted genes were identified. Most of these predicted genes are expressed only in embryonic stages. Analyses of the genomic region adjacent to proximal CMT1A-REP indicated an evolutionary mechanism for the formation of proximal CMT1A-REP and the creation of novel genes by DNA rearrangement during primate speciation.
The 1.4-Mb CMT1A Duplication/HNPP Deletion Genomic Region Reveals Unique Genome Architectural Features and Provides Insights into the Recent Evolution of New Genes
Ken Inoue,1 Ken Dewar,3 Nicholas Katsanis,1 Lawrence T. Reiter,1,4 Eric S. Lander,3 Keri L. Devon,3 Dudley W. Wyman,3 James R. Lupski,1,2,5 and Bruce Birren3
Sub‐Saharan Africa (SSA) could face food shortages in the future because of its growing population. Agricultural expansion causes forest degradation in SSA through livestock grazing, reducing forest carbon (C) sinks and increasing greenhouse gas (GHG) emissions. Therefore, intensification should produce more food while reducing pressure on forests. This study assessed the potential for the dairy sector in Kenya to contribute to low‐emissions development by exploring three feeding scenarios. The analyses used empirical spatially explicit data, and a simulation model to quantify milk production, agricultural emissions and forest C loss due to grazing. The scenarios explored improvements in forage quality (Fo), feed conservation (Fe) and concentrate supplementation (Co): FoCo fed high‐quality Napier grass (Pennisetum purpureum), FeCo supplemented maize silage and FoFeCo a combination of Napier, silage and concentrates. Land shortages and forest C loss due to grazing were quantified with land requirements and feed availability around forests. All scenarios increased milk yields by 44%-51%, FoCo reduced GHG emission intensity from 2.4 ± 0.1 to 1.6 ± 0.1 kg CO2eq per kg milk, FeCo reduced it to 2.2 ± 0.1, whereas FoFeCo increased it to 2.7 ± 0.2 kg CO2eq per kg milk because of land use change emissions. Closing the yield gap of maize by increasing N fertilizer use reduced emission intensities by 17% due to reduced emissions from conversion of grazing land. FoCo was the only scenario that mitigated agricultural and forest emissions by reducing emission intensity by 33% and overall emissions by 2.5% showing that intensification of dairy in a low‐income country can increase milk yields without increasing emissions. There are, however, risks of C leakage if agricultural and forest policies are not aligned leading to loss of forest to produce concentrates. This approach will aid the assessment of the climate‐smartness of livestock production practices at the national level in East Africa.
forest disturbance, greenhouse gas emissions, livestock grazing, LivSim, smallholder farming, sustainable intensification
Intensification of dairy production can increase the GHG mitigation potential of the land use sector in East Africa
Patric Brandt, 1 , 2 Gabriel Yesuf, 3 Martin Herold, 2 and Mariana C. Rufinocorresponding author 1 , 3
The characterization of soil is essential for the evaluation of seismic hazard, because soil properties strongly influence the damage caused by earthquakes. Methods based on seismic noise are the most commonly used in soil characterization. Concretely, methods based on seismic noise array measurements allow for the estimation of Rayleigh wave dispersion curves and, subsequently, shear-wave velocity profiles. The equipment required for the application of this technique is usually very expensive, which could be a significant economic challenge for small research groups. In this work, we have developed a wireless multichannel seismic noise recorder system (Geophonino-W), which is suitable for array measurements. Each station includes a microcontroller board (Arduino), a conditioning circuit, an Xbee module, an SD card, and a GPS module. Several laboratory tests were carried out in order to study the performance of the Geophonino-W: A frequency response test (impulse response and noise); synchronization test; and battery duration test. Comparisons of Geophonino-W with the commercial systems and field measurements were also carried out. The estimated dispersion curves obtained using the proposed system were compared with the ones obtained using other commercial equipment, demonstrating the effectiveness of Geophonino-W for seismic noise array measurements. Geophonino-W is an economic open-source and hardware system that is available to any small research group or university.
seismic data acquisition, seismic noise measurement, Arduino Due, ambient-noise recorder, customized hardware, seismic signal conditioning circuit
Geophonino-W: A Wireless Multichannel Seismic Noise Recorder System for Array Measurements
Juan Luis Soler-Llorens,1,* Juan Jose Galiana-Merino,2,3 Jose Juan Giner-Caturla,1,3 Sergio Rosa-Cintas,3,4 and Boualem Youcef Nassim-Benabdeloued2,5