Comparative Analysis of Fatty Acid Desaturases in Cyanobacterial Genomes

Fatty acid desaturases are enzymes that introduce double bonds into the hydrocarbon chains of fatty acids. The fatty acid desaturases from 37 cyanobacterial genomes were identified and classified based upon their conserved histidine-rich motifs and phylogenetic analysis, which help to determine the amounts and distributions of desaturases in cyanobacterial species. The filamentous or N2-fixing cyanobacteria usually possess more types of fatty acid desaturases than that of unicellular species. The pathway of acyl-lipid desaturation for unicellular marine cyanobacteria Synechococcus and Prochlorococcus differs from that of other cyanobacteria, indicating different phylogenetic histories of the two genera from other cyanobacteria isolated from freshwater, soil, or symbiont. Strain Gloeobacter violaceus PCC 7421 was isolated from calcareous rock and lacks thylakoid membranes. The types and amounts of desaturases of this strain are distinct to those of other cyanobacteria, reflecting the earliest divergence of it from the cyanobacterial line. Three thermophilic unicellular strains, Thermosynechococcus elongatus BP-1 and two Synechococcus Yellowstone species, lack highly unsaturated fatty acids in lipids and contain only one Δ9 desaturase in contrast with mesophilic strains, which is probably due to their thermic habitats. Thus, the amounts and types of fatty acid desaturases are various among different cyanobacterial species, which may result from the adaption to environments in evolution

Insights into the provenance of the Chinese Loess Plateau from joint zircon U-Pb and garnet geochemical analysis of last glacial loess

The Chinese Loess Plateau, the world’s largest and oldest loess record, preserves evidence of Asia’s long-term dust source dynamics, but there is uncertainty over the source of the deposits. Recent single-grain detrital zircon U-Pb age analysis has progressed this issue, but debates remain about source changes, and the generation and interpretation of zircon data. To address this, we analyze different groupings of new and existing datasets from the Loess Plateau and potential sources. We also present the results of a first high resolution sampling, multi-proxy provenance analysis of Beiguoyuan loess using U-Pb dating of detrital zircons and detrital garnet geochemistry. The data shows that some small source differences seem to exist between different areas on the Loess Plateau. However, sediment source appears to be unchanging between loess and palaeosols, supporting a recent material recycling hypothesis. Our zircon and garnet data demonstrates, however, that Beiguoyuan experienced a temporary, abrupt source shift during the last glacial maximum, implying that local dust sources became periodically active during the Quaternary. Our results highlight that grouping data to achieve bigger datasets could cause identification of misleading trends. Additionally, we suggest that multi-proxy single-grain approaches are required to gain further insight into Chinese Loess Plateau dust sources

On the Effectiveness of Speech Self-supervised Learning for Music

Self-supervised learning (SSL) has shown promising results in various speech and natural language processing applications. However, its efficacy in music information retrieval (MIR) still remains largely unexplored. While previous SSL models pre-trained on music recordings may have been mostly closed-sourced, recent speech models such as wav2vec2.0 have shown promise in music modelling. Nevertheless, research exploring the effectiveness of applying speech SSL models to music recordings has been limited. We explore the music adaption of SSL with two distinctive speech-related models, data2vec1.0 and Hubert, and refer to them as music2vec and musicHuBERT, respectively. We train $12$ SSL models with 95M parameters under various pre-training configurations and systematically evaluate the MIR task performances with 13 different MIR tasks. Our findings suggest that training with music data can generally improve performance on MIR tasks, even when models are trained using paradigms designed for speech. However, we identify the limitations of such existing speech-oriented designs, especially in modelling polyphonic information. Based on the experimental results, empirical suggestions are also given for designing future musical SSL strategies and paradigms

MERT: Acoustic Music Understanding Model with Large-Scale Self-supervised Training

Self-supervised learning (SSL) has recently emerged as a promising paradigm for training generalisable models on large-scale data in the fields of vision, text, and speech. Although SSL has been proven effective in speech and audio, its application to music audio has yet to be thoroughly explored. This is primarily due to the distinctive challenges associated with modelling musical knowledge, particularly its tonal and pitched characteristics of music. To address this research gap, we propose an acoustic Music undERstanding model with large-scale self-supervised Training (MERT), which incorporates teacher models to provide pseudo labels in the masked language modelling (MLM) style acoustic pre-training. In our exploration, we identified a superior combination of teacher models, which outperforms conventional speech and audio approaches in terms of performance. This combination includes an acoustic teacher based on Residual Vector Quantization - Variational AutoEncoder (RVQ-VAE) and a musical teacher based on the Constant-Q Transform (CQT). These teachers effectively guide our student model, a BERT-style transformer encoder, to better model music audio. In addition, we introduce an in-batch noise mixture augmentation to enhance the representation robustness. Furthermore, we explore a wide range of settings to overcome the instability in acoustic language model pre-training, which allows our designed paradigm to scale from 95M to 330M parameters. Experimental results indicate that our model can generalise and perform well on 14 music understanding tasks and attains state-of-the-art (SOTA) overall scores. The code and models are online: https://github.com/yizhilll/MERT

Tipping Points in Seaweed Genetic Engineering: Scaling Up Opportunities in the Next Decade

Seaweed genetic engineering is a transgenic expression system with unique features compared with those of heterotrophic prokaryotes and higher plants. This study discusses several newly sequenced seaweed nuclear genomes and the necessity that research on vector design should consider endogenous promoters, codon optimization, and gene copy number. Seaweed viruses and artificial transposons can be applied as transformation methods after acquiring a comprehensive understanding of the mechanism of viral infections in seaweeds and transposon patterns in seaweed genomes. After cultivating transgenic algal cells and tissues in a photobioreactor, a biosafety assessment of genetically modified (GM) seaweeds must be conducted before open-sea application. We propose a set of programs for the evaluation of gene flow from GM seaweeds to local/geographical environments. The effective implementation of such programs requires fundamentally systematic and interdisciplinary studies on algal physiology and genetics, marine hydrology, reproductive biology, and ecology.;Seaweed genetic engineering is a transgenic expression system with unique features compared with those of heterotrophic prokaryotes and higher plants. This study discusses several newly sequenced seaweed nuclear genomes and the necessity that research on vector design should consider endogenous promoters, codon optimization, and gene copy number. Seaweed viruses and artificial transposons can be applied as transformation methods after acquiring a comprehensive understanding of the mechanism of viral infections in seaweeds and transposon patterns in seaweed genomes. After cultivating transgenic algal cells and tissues in a photobioreactor, a biosafety assessment of genetically modified (GM) seaweeds must be conducted before open-sea application. We propose a set of programs for the evaluation of gene flow from GM seaweeds to local/geographical environments. The effective implementation of such programs requires fundamentally systematic and interdisciplinary studies on algal physiology and genetics, marine hydrology, reproductive biology, and ecology.</p

Advances in genetic engineering of marine algae

Algae are a component of bait sources for animal aquaculture, and they produce abundant valuable compounds for the chemical industry and human health. With today's fast growing demand for algae biofuels and the profitable market for cosmetics and pharmaceuticals made from algal natural products, the genetic engineering of marine algae has been attracting increasing attention as a crucial systemic technology to address the challenge of the biomass feedstock supply for sustainable industrial applications and to modify the metabolic pathway for the more efficient production of high-value products. Nevertheless, to date, only a few marine algae species can be genetically manipulated. In this article, an updated account of the research progress in marine algal genomics is presented along with methods for transformation. In addition, vector construction and gene selection strategies are reviewed. Meanwhile, a review on the progress of bioreactor technologies for marine algae culture is also revisited. (c) 2012 Elsevier Inc. All rights reserved.Algae are a component of bait sources for animal aquaculture, and they produce abundant valuable compounds for the chemical industry and human health. With today's fast growing demand for algae biofuels and the profitable market for cosmetics and pharmaceuticals made from algal natural products, the genetic engineering of marine algae has been attracting increasing attention as a crucial systemic technology to address the challenge of the biomass feedstock supply for sustainable industrial applications and to modify the metabolic pathway for the more efficient production of high-value products. Nevertheless, to date, only a few marine algae species can be genetically manipulated. In this article, an updated account of the research progress in marine algal genomics is presented along with methods for transformation. In addition, vector construction and gene selection strategies are reviewed. Meanwhile, a review on the progress of bioreactor technologies for marine algae culture is also revisited. (c) 2012 Elsevier Inc. All rights reserved