14 Works

Data from: Signatures of divergence, invasiveness and terrestralization revealed by four apple snail genomes

Jin Sun, Huawei Mu, Jack C. H. Ip, Runsheng Li, Ting Xu, Alice Accorsi, Alejandro Sánchez Alvarado, Eric Ross, Yi Lan, Yanan Sun, Alfredo Castro-Vazquez, Israel A. Vega, Horacio Heras, Santiago Ituarte, Bert Van Bocxlaer, Kenneth A. Hayes, Robert H. Cowie, Zhongying Zhao, Yu Zhang, Pei-Yuan Qian & Jian-Wen Qiu
The family Ampullariidae includes both aquatic and amphibious apple snails. They are an emerging model for evolutionary studies due to the high diversity, ancient history and wide geographical distribution. Insight into drivers of ampullariid evolution is hampered, however, by the lack of genomic resources. Here we report the genomes of four ampullariids spanning the Old World (Lanistes nyassanus) and New World (Pomacea canaliculata, Pomacea maculata and Marisa cornuarietis) clades. The ampullariid genomes have conserved ancient...

Data from: De novo assembly of the transcriptome of an invasive snail and its multiple ecological applications

Jin Sun, Mingling Wang, Hao Wang, Huoming Zhang, Xianglong Zhang, Vengatesen Thiyagarajan, Pei-Yuan Qian, Jian-Wen Qiu, J. W. Qiu & P. Y. Qian
Studying how invasive species respond to environmental stress at the molecular level can help us assess their impact and predict their range expansion. Development of markers of genetic polymorphism can help us reconstruct their invasive route. However, to conduct such studies requires the presence of substantial amount of genomic resources. This study aimed to generate and characterize genomic resources using high throughput transcriptome sequencing for Pomacea canaliculata, a non-model gastropod indigenous to Argentina that has...

Data from: Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes

Jin Sun, Yu Zhang, Ting Xu, Yang Zhang, Huawei Mu, Yanjie Zhang, Yi Lan, Christopher J. Fields, Jerome H. L. Hui, Wei-Peng Zhang, Runsheng Li, Wenyan Nong, Fiona K. M. Cheung, Jian-Wen Qiu & Pei-Yuan Qian
Hydrothermal vents and methane seeps are extreme deep-sea ecosystems that support dense populations of specialised macrobenthos such as mussels. But lack of genome information hinders understanding of the adaptation of these animals to such inhospitable environment. Here we report the genomes of a deep-sea vent/seep mussel Bathymodiolus platifrons and a shallow-water mussel Modiolus philippinarum. Phylogenetic analysis shows that these mussel species diverged approximately 110.4 million years ago. Many gene families, especially those for stabilising protein...

Data from: Zebrafish retinal ganglion cells asymmetrically encode spectral and temporal information across visual space

Paul A. Roberts, Mingyi Zhou, John Bear, Filip K. Janiak, Julie Semmelhack, Takeshi Yoshimatsu & Tom Baden
In vertebrate vision, the tetrachromatic larval zebrafish permits non-invasive monitoring and manipulating of neural activity across the nervous system in vivo during ongoing behaviour. However, despite a perhaps unparalleled understanding of links between zebrafish brain circuits and visual behaviours, comparatively little is known about what their eyes send to the brain via retinal ganglion cells (RGCs). Major gaps in knowledge include any information on spectral coding, and information on potentially critical variations in RGC properties...

Signature of a pair of Majorana zero modes in superconducting gold surface states

Peng Wei, Sujit Manna, Yingming Xie, Kam Tuen Law, Patrick Lee & Jagadeesh Moodera
Under certain conditions, a fermion in a superconductor can separate in space into two parts known as Majorana zero modes, which are immune to decoherence from local noise sources and are attractive building blocks for quantum computers. Promising experimental progress has been made to demonstrate Majorana zero modes in materials with strong spin-orbit coupling proximity coupled to superconductors. Here we show direct evidence of the split Majorana pair in a new material platform utilizing the...

Three-Dimensional Numerical Modeling of a Scroll Vortex Intake

S. N. Chan
Scroll vortex intakes are vortex drop structures commonly used in water supply, drainage and sewerage systems, characterized by a vortex chamber with its wall curling inwards to the dropshaft and a horizontal bottom. The stormwater flows into the intake via an eccentrical approach channel, which imparts vortex motion to the flow, forming a swirling vortex flow with a stable air core through the center of dropshaft. Over past decades, much effort has been devoted to...

Data from: Genome reduction and microbe-host interactions drive adaptation of a sulfur-oxidizing bacterium associated with a cold seep sponge

Ren-Mao Tian, Weipeng Zhang, Lin Cai, Yue-Him Wong, Wei Ding & Pei-Yuan Qian
As the most ancient metazoan, sponges have established close relationships with particular microbial symbionts. However, the characteristics and physiology of thioautotrophic symbionts in deep-sea sponges are largely unknown. Using a tailored “differential coverage binning” method on 22-Gb metagenomic sequences, we recovered the nearly complete genome of a sulfur-oxidizing bacterium (SOB) that dominates the microbiota of the cold seep sponge Suberites sp. Phylogenetic analyses suggested that this bacterium (an unclassified gammaproteobacterium termed “Gsub”) may represent a...

Data from: Understanding the transition from water to land: insights from multi-omic analyses of the perivitelline fluid of apple snail eggs

Jack C.H. Ip, Huawei Mu, Yanjie Zhang, Jin Sun, Horacio Heras, Ka Hou Chu & Jian-Wen Qiu
Most gastropods deposit their eggs either on land or underwater, but the family Ampullariidae includes members that exhibit both underwater and aerial oviposition, making it an ideal model for understanding mechanisms underlying the evolutionary transition from water to land. We applied SDS-PAGE and LC-MS/MS to analyse the proteome of the egg perivitelline fluid (PVF) of Marisa cornuarietis – an aquatic ovipositing ampullariid. Comparison with the reported PVF proteomes of two aerial ovipositing ampullariids (Pomacea canaliculata...

Raw images of targeted gearshifting in actin-based active nematic liquid crystals

Steven Redford, Rui Zhang, Paul Ruijgrok, Nitin Kumar, Ali Mozaffari, Sasha Zemsky, Aaron Dinner, Vincenzo Vitelli, Zev Bryant, Margaret Gardel & Juan De Pablo
Active materials are capable of converting free energy into mechanical work to produce autonomous motion, and exhibit striking collective dynamics that biology relies on for essential functions. Controlling those dynamics and transport in synthetic systems has been particularly challenging. Here, we introduce the concept of spatially structured activity as a means to control and manipulate transport in active nematic liquid crystals consisting of actin filaments and light-sensitive myosin motors. Simulations and experiments are used to...

Data from: AmpuBase: a transcriptome database for eight species of apple snails (Gastropoda: Ampullariidae)

Jack C. H. Ip, Huawei Mu, Qian Chen, Jin Sun, Santiago Ituarte, Horacio Heras, Bert Van Bocxlaer, Monthon Ganmanee, Xin Huang & Jian-Wen Qiu
Background: Gastropoda, with approximately 80,000 living species, is the largest class of Mollusca. Among gastropods, apple snails (family Ampullariidae) have members that are widely distributed in tropical and subtropical freshwater ecosystems and are ecologically and economically important. They exhibit various morphological and physiological adaptations to their respective habitats, which make them ideal candidates for studying adaptation, population divergence, speciation, and larger-scale patterns of diversity, including biogeography of native and invasive populations. The limited availability of...

Data from: Environmental switching during biofilm development in a cold seep system and functional determinants of species sorting

Weipeng Zhang, Renmao Tian, Yang Bo, Huiluo Cao, Lin Cai, Lianguo Chen, Guowei Zhou, Jin Sun, Xixiang Zhang, Abdulaziz Al-Suwailem & Pei-Yuan Qian
The functional basis for species sorting theory remains elusive, especially for microbial community assembly in deep-sea environments. Using artificial surface-based biofilm models, our recent work revealed taxonomic succession during biofilm development in a newly defined cold seep system, the Thuwal cold seeps II, which comprises a brine pool and the adjacent normal bottom water (NBW) to form a metacommunity via the potential immigration of organisms from one patch to another. Here, we designed an experiment...

Data from: Halloysite nanotube-based electrospun ceramic nanofibre mat: a novel support for zeolite membranes

Zhuwen Chen, Jiaying Zeng, Dong Lv, Jinqiang Gao, Jian Zhang, Shan Bai, Ruili Li, Mei Hong & Jingshen Wu
Some key parameters of supports such as porosity, pore shape and size are of great importance for fabrication and performance of zeolite membranes. In this study, we fabricated millimetre-thick, self-standing electrospun ceramic nanofibre mats and employed them as a novel support for zeolite membranes. The nanofibre mats were prepared by electrospinning a halloysite nanotubes/polyvinyl pyrrolidone composite followed by a programmed sintering process. The interwoven nanofibre mats possess up to 80% porosity, narrow pore size distribution,...

Niche differences in co-occurring cryptic coral species (Pocillopora spp.)

Erika Johnston, Alex Wyatt, James Leichter & Scott Burgess
Cryptic species that are morphologically similar co-occur because either the rate of competitive exclusion is very slow, or because they are not, in fact, ecologically similar. The processes that maintain cryptic local diversity may, therefore, be particularly subtle and difficult to identify. Here, we uncover differences among several cryptic species in their relative abundance across a depth gradient within a dominant and ecologically important genus of hard coral, Pocillopora. From extensive sampling unbiased towards morphological...

Response diversity in corals: hidden differences in bleaching mortality among cryptic Pocillopora species

Scott Burgess, Erika Johnston, Alex Wyatt, James Leichter & Peter Edmunds
Variation among functionally similar species in their response to environmental stress buffers ecosystems from changing states. Functionally similar species may often be cryptic species representing evolutionarily distinct genetic lineages that are morphologically indistinguishable. However, the extent to which cryptic species differ in their response to stress, and could therefore provide a source of response diversity, remains unclear because they are often not identified or are assumed to be ecologically equivalent. Here, we uncover differences in...

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