Geology topics

Chen Yang

Publications and source records attributed to Chen Yang.

3 recordsLinked to original sources

USGS2024

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, the consortium generated over 427 million long-read sequences from complementary DNA and direct RNA datasets, encompassing human, mouse and manatee species. Developers utilized these data to address challenges in transcript isoform detection, quantification and de novo transcript detection. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. Incorporating additional orthogonal data and replicate samples is advised when aiming to detect rare and novel transcripts or using reference-free approaches. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.

Nature Methods↗

USGS2021

Sap flow evidence of chilling injury and recovery in mangroves following a spring cold spell

Mangroves are periodically influenced in negative ways by non-freezing temperatures across their global sub-tropical range. However, physiological and morphological evidence of chilling influences to non-freezing chilling events has not been measured in field settings. In this study, we measured sap flow ( J s ) during such a chilling (but non-freezing) event in southern China and documented the reductions in J s and the recovery that ensued. We calculated tree water use (TWU) from J s measurements taken from thermal dissipation sap flow sensors on two mangrove species ( Sonneratia apetala and S. caseolaris ). This chilling event significantly injured the mangrove trees in the form of leaf scorch and massive defoliation. Diurnal variations of stem J s of both species were altered significantly after chilling. On the day of the chilling event, J s of S. caseolaris was reduced from the daily maximum of 44.1 g H 2 O m −2 s −1 to 0 immediately after chilling, which lasted throughout the remainder of the day. In contrast, S. apetala showed a certain low-temperature tolerance, while still maintaining an adequate transpiration rate after chilling, indicative of a more resilient hydraulic transport system to low temperatures. The sap flow data collected revealed substantial evidence for acute water conservation during low-temperature events, perhaps ameliorating low-temperature damage. Hence, the responses of some mangrove species with high sensitivity to low, but non-freezing, temperature (such as S. caseolaris ) may indicate that mangroves possess adaptive whole-tree strategies to cold temperature.

Trees: Structure and Function↗

USGS2019

Clustered BSRs: Evidence for gas hydrate-bearing turbidite complexes in folded regions, example from the Perdido Fold Belt, northern Gulf of Mexico

We describe previously undocumented but extensive gas hydrate accumulations in the mouth of Perdido Canyon in the northern Gulf of Mexico. The accumulations are located within central parts of structural domes (four-way closures) and are characterized by stacked, high-amplitude bottom simulating reflections (BSRs) that we call clustered BSRs. Seismic data from Perdido Canyon show two clustered BSRs associated with turbidite sequences within two dome folds formed from tectonic folding and salt diapir rise. The northwestern (NW) and southeastern (SE) clustered BSRs have aerial extents of ~25 km2 and 50 km2, respectively. Well log data confirm gas hydrate occurs above the NW clustered BSR, within a 225 m-thick consistently high-resistivity interval that we interpret as gas hydrate in near-vertical fractures and turbidite sands. The SE dome is only drilled at the edge of the BSR; nevertheless, the well log data indicate that a 30 m-thick gas hydrate accumulation is present. Gas chromatographic logs in both domes suggest a gradual transition from predominantly microbial gas below the BSR (500–1000 meters below seafloor (mbsf)) to thermogenic gas at 1000–2000 mbsf. Based on the well log data and seismic stratigraphic analysis, we find gas hydrate is concentrated in fractures in marine mud, as well as in the pores of submarine fan turbidities, where saturations reach as high as 75%. An estimate of the total gas hydrate-bound gas volume at standard temperature and pressure is between 0.04 and 0.17 trillion cubic meters (TCM) assuming average hydrate saturation of 5-20% in a ~45 m thick turbidite sand unit above the Perdido Canyon BSR area. Measured BSR extent and gas volume estimates indicate that the NW and SE reservoirs are among the largest gas hydrate occurrences known in the Gulf of Mexico.

Perdido Fold Belt↗