Transcriptome innovations in primates revealed by single-molecule long-read sequencing.

Transcriptomic diversity greatly contributes to the fundamentals of disease, lineage-specific biology, and environmental adaptation. However, much of the actual isoform repertoire contributing to shaping primate evolution remains unknown. Here, we combined deep long- and short-read sequencing complemented with mass spectrometry proteomics in a panel of lymphoblastoid cell lines (LCLs) from human, three other great apes, and rhesus macaque, producing the largest full-length isoform catalog in primates to date. Around half of the captured isoforms are not annotated in their reference genomes, significantly expanding the gene models in primates. Furthermore, our comparative analyses unveil hundreds of transcriptomic innovations and isoform usage changes related to immune function and immunological disorders. The confluence of these evolutionary innovations with signals of positive selection and their limited impact in the proteome points to changes in alternative splicing in genes involved in immune response as an important target of recent regulatory divergence in primates.

Genetic and preimplantation diagnosis of cystic kidney disease with ventriculomegaly.

Ventriculomegaly with cystic kidney disease (VMCKD) is a rare and severe disorder characterized by cerebral ventriculomegaly, greatly elevated maternal serum alpha-fetoprotein (MSAFP) or amniotic fluid alpha-fetoprotein (AFAFP) levels and kidney disease similar to Finnish congenital nephrosis. Recessive mutations in the CRB2 (NM_173689) gene have been shown to cause the syndrome. Here, we described a nonconsanguineous Chinese family with two fetuses affected with VMCKD. A novel compound heterozygous mutation was identified in the CRB2 gene with co-segregation. One mutation [c.1960G>C (p.A654P)] was inherited from the father, while another mutation [c.3078_c.3093delGGCGCGGCCCCGGCCC (p.L1026Lfs*110)] was inherited from the mother. Preimplantation genetic testing for monogenic disease (PGT-M) was performed for the carrier couple with full informed consent and successfully blocked the inheritance of the disease. Our study has important implications on molecular diagnosis and genetic counseling for VMCKD and extends the mutation spectrum in CRB2 gene.

Chemoselective Hydrosilylation of the α,ß-Site Double Bond in α,ß- and α,ß,γ,δ-Unsaturated Ketones Catalyzed by Macrosteric Borane Promoted by Hexafluoro-2-propanol.

The B(C6F5)3-catalyzed chemoselective hydrosilylation of α,ß- and α,ß,γ,δ-unsaturated ketones into the corresponding non-symmetric ketones in mild reaction conditions is developed. Nearly 55 substrates including those bearing reducible functional groups such as alkynyl, alkenyl, cyano, and aromatic heterocycles are chemoselectively hydrosilylated in good to excellent yields. Isotope-labeling studies revealed that hexafluoro-2-propanol also served as a hydrogen source in the process.

[Adaptive EEMD residue related baseline correction algorithm].

Baseline correction is an important part of spectral analysis; the existing algorithms usually need to set the key parameters and does not have adaptability. The spectral baseline is fitted by the residue according to the feature of ensemble empirical mode decomposition (EEMD for short). The correlation between residual and original signal, the self-correlation and the cross-correlation of residual form the residual related rule. The residual related rule is proposed to judge whether the residual is a component of baseline, based on which adaptive EEMD residual related base line algorithm is proposed. With experiment on the simulated spectrum data of superimposing curve background and the linear background, the results showed that in the case of known baseline mathematical assumption: EEMD residual related method is not so good for polynomial fitting, it is almost no difference from linear fitting, but is better than the wavelet decomposition. In the absence of spectral background knowledge, the real Raman spectrum data are tested. The model is established between Raman spectra treated by the procedure above and chlorophyll, and the model corrected by EEMD residual related baseline method has the biggest correlation coefficient and prediction coefficient, but the smallest root mean square error of cross validation and relative prediction deviation. The effect of EEMD residual related baseline method effects on the peak position, peak intensity and peak width is the smallest in all kinds of baseline correction methods. EEMD residual method has the best baseline correction effect. Experiments show that this algorithm can be used for Raman spectra baseline correction, without prior knowledge of the sample composition analysis, and there is no need to select appropriate fitting function, fitting data points, fitting order as well as basis function and decomposition levels, also there is no need of mathematical hypothesis of baseline signal distribution, so the adaptability is very strong.

Effect of freeze‒thaw cycles on root-Soil composite mechanical properties and slope stability.

Natural disasters such as landslides often occur on soil slopes in seasonally frozen areas that undergo freeze‒thaw cycling. Ecological slope protection is an effective way to prevent such disasters. To explore the change in the mechanical properties of soil under the influence of both root reinforcement and freeze‒thaw cycles and its influence on slope stability, the Baijiabao landslide in the Three Gorges Reservoir area was taken as an example. The mechanical properties of soil under different confining pressures, vegetation coverages (VCs) and numbers of freeze‒thaw cycles were studied via mechanical tests, such as triaxial compression tests, wave velocity tests and FLAC3D simulations. The results show that the shear strength of a root-soil composite increases with increasing confining pressure and VC and decreases with increasing number of freeze‒thaw cycles. Bermuda grass roots and confining pressure jointly improve the durability of soil under freeze‒thaw conditions. However, with an increase in the number of freeze‒thaw cycles, the resistance of root reinforcement to freeze‒thaw action gradually decreases. The observed effect of freeze‒thaw cycles on soil degradation was divided into three stages: a significant decrease in strength, a slight decrease in strength and strength stability. Freeze‒thaw cycles and VC mainly affect the cohesion of the soil and have little effect on the internal friction angle. Compared with that of a bare soil slope, the safety factor of a slope covered with plants is larger, the maximum displacement of a landslide is smaller, and it is less affected by freezing and thawing. These findings can provide a reference for research on ecological slope protection technology.

Composition of inorganic elements in fine particulate matter emitted during surface fire in relation to moisture content of forest floor combustibles.

The moisture content of combustible material on the forest floor is constantly changing due to environmental factors, which have a direct impact on the composition and emission intensity of particulate matter released during fire. In this study, an indoor biomass combustion analysis device was used to analyze the emission characteristics of fine particulate matter (PM2.5) from combustion of herbaceous combustible materials with different moisture contents (0%, 15%, and 30%). The composition of inorganic elements in PM2.5 (Zn, K, Mg, Ca, and other 13 measurable elements) were determined by inductively coupled plasma-mass spectrometer (ICP-MS). The results showed that the PM2.5 emission factor increased significantly with the increase of moisture content of combustible materials in the range of 11.63 ± 0.55 for dry samples to 36.71 ± 1.21 g/kg for samples with 30% moisture content. The main elemental components of PM2.5 were K, Zn, Ca, Mg, and Na and K, Ca, Mg, and Na emission factors increased with the increase of moisture content of combustibles. The proportion of macronutrients in PM2.5 released by combustion of each herb increased as the moisture content increased, but the proportion of trace elements gradually decreased. There was a good correlation between elemental composition of PM2.5 and that of herbaceous combustibles. The results provide evidence that the moisture content of combustible materials has a significant effect on the emission of inorganic elements in particulate matter, and hence cautions should be exercised during fuel reduction treatments, such as early prescribed fire.

On the origin and evolution of RNA editing in metazoans.

Extensive adenosine-to-inosine (A-to-I) editing of nuclear-transcribed mRNAs is the hallmark of metazoan transcriptional regulation. Here, by profiling the RNA editomes of 22 species that cover major groups of Holozoa, we provide substantial evidence supporting A-to-I mRNA editing as a regulatory innovation originating in the last common ancestor of extant metazoans. This ancient biochemistry process is preserved in most extant metazoan phyla and primarily targets endogenous double-stranded RNA (dsRNA) formed by evolutionarily young repeats. We also find intermolecular pairing of sense-antisense transcripts as an important mechanism for forming dsRNA substrates for A-to-I editing in some but not all lineages. Likewise, recoding editing is rarely shared across lineages but preferentially targets genes involved in neural and cytoskeleton systems in bilaterians. We conclude that metazoan A-to-I editing might first emerge as a safeguard mechanism against repeat-derived dsRNA and was later co-opted into diverse biological processes due to its mutagenic nature.

Eighty million years of rapid evolution of the primate Y chromosome.

The Y chromosome usually plays a critical role in determining male sex and comprises sequence classes that have experienced unique evolutionary trajectories. Here we generated 19 new primate sex chromosome assemblies, analysed them with 10 existing assemblies and report rapid evolution of the Y chromosome across primates. The pseudoautosomal boundary has shifted at least six times during primate evolution, leading to the formation of a Simiiformes-specific evolutionary stratum and to the independent start of young strata in Catarrhini and Platyrrhini. Different primate lineages experienced different rates of gene loss and structural and chromatin change on their Y chromosomes. Selection on several Y-linked genes has contributed to the evolution of male developmental traits across the primates. Additionally, lineage-specific expansions of ampliconic regions have further increased the diversification of the structure and gene composition of the Y chromosome. Overall, our comprehensive analysis has broadened our knowledge of the evolution of the primate Y chromosome.

Labour classified by cervical dilatation & fetal membrane rupture demonstrates differential impact on RNA-seq data for human myometrium tissues.

High throughput sequencing has previously identified differentially expressed genes (DEGs) and enriched signalling networks in human myometrium for term (≥37 weeks) gestation labour, when defined as a singular state of activity at comparison to the non-labouring state. However, transcriptome changes that occur during transition from early to established labour (defined as ≤3 and >3 cm cervical dilatation, respectively) and potentially altered by fetal membrane rupture (ROM), when adapting from onset to completion of childbirth, remained to be defined. In the present study, we assessed whether differences for these two clinically observable factors of labour are associated with different myometrial transcriptome profiles. Analysis of our tissue ('bulk') RNA-seq data (NCBI Gene Expression Omnibus: GSE80172) with classification of labour into four groups, each compared to the same non-labour group, identified more DEGs for early than established labour; ROM was the strongest up-regulator of DEGs. We propose that lower DEGs frequency for early labour and/or ROM negative myometrium was attributed to bulk RNA-seq limitations associated with tissue heterogeneity, as well as the possibility that processes other than gene transcription are of more importance at labour onset. Integrative analysis with future data from additional samples, which have at least equivalent refined clinical classification for labour status, and alternative omics approaches will help to explain what truly contributes to transcriptomic changes that are critical for labour onset. Lastly, we identified five DEGs common to all labour groupings; two of which (AREG and PER3) were validated by qPCR and not differentially expressed in placenta and choriodecidua.

Limits to the cellular control of sequestered cryptophyte prey in the marine ciliate Mesodinium rubrum.

The marine ciliate Mesodinium rubrum is famous for its ability to acquire and exploit chloroplasts and other cell organelles from some cryptophyte algal species. We sequenced genomes and transcriptomes of free-swimming Teleaulax amphioxeia, as well as well-fed and starved M. rubrum in order to understand cellular processes upon sequestration under different prey and light conditions. From its prey, the ciliate acquires the ability to photosynthesize as well as the potential to metabolize several essential compounds including lysine, glycan, and vitamins that elucidate its specific prey dependency. M. rubrum does not express photosynthesis-related genes itself, but elicits considerable transcriptional control of the acquired cryptophyte organelles. This control is limited as light-dependent transcriptional changes found in free-swimming T. amphioxeia got lost after sequestration. We found strong transcriptional rewiring of the cryptophyte nucleus upon sequestration, where 35% of the T. amphioxeia genes were significantly differentially expressed within well-fed M. rubrum. Qualitatively, 68% of all genes expressed within well-fed M. rubrum originated from T. amphioxeia. Quantitatively, these genes contributed up to 48% to the global transcriptome in well-fed M. rubrum and down to 11% in starved M. rubrum. This tertiary endosymbiosis system functions for several weeks, when deprived of prey. After this point in time, the ciliate dies if not supplied with fresh prey cells. M. rubrum represents one evolutionary way of acquiring photosystems from its algal prey, and might represent a step on the evolutionary way towards a permanent tertiary endosymbiosis.

Author Correction: Neuroprotectants attenuate hypobaric hypoxia-induced brain injuries in cynomolgus monkeys.

Following the publication of our paper (Zhang et al., 2020), it has come to our attention that we erroneously listed two funding sources unrelated to this study in the "ACKNOWLEDGEMENTS" section. Hereby, we wish to update the "ACKNOWLEDGEMENTS" section as a correction.

Dehydration in water: frustrated Lewis pairs directly catalyzed allylization of electron-rich arenes and allyl alcohols.

A frustrated Lewis pair (FLP)-catalyzed allylation of allyl alcohols with electron-rich arenes has been developed. Interestingly, in this reaction, the electron-rich arenes and allyl alcohols are dehydrated in water. What's more, water was the sole byproduct of the reaction. In this protocol, various allyl alcohols can be converted into allyl cations and attacked by the electron-rich arenes to form aryl cation intermediates. Finally, the aryl cation intermediates are deprotonated to give the 1,3-diarylpropenes. In this protocol, indole allyl alcohols can undergo a bimolecular ring closure reaction, and structurally diverse tetrahydroindolo[3,2-b]carbazoles could be smoothly obtained. The reaction is not sensitive to oxygen and has been performed on a gram-scale.

Cobalt-Catalyzed Cycloamination: Synthesis and Photophysical Properties of Polycyclic N-Heterocycles.

The first earth-abundant cobalt-catalyzed cycloamination of indolylquinones and various (hetero)aromatic amine under ligand-free conditions for the synthesis of polycyclic N-heterocycles has been developed. The process allows facile access to polycyclic N-heterocycles with tolerance of chloride, bromide, amino, thio, etc. groups in moderate to high yields (up to 89%). In addition, The photophysical properties of the synthesized products were evaluated. These products exhibit interesting fluorescence properties, which is promising for fluorescent probes.

Neuroprotectants attenuate hypobaric hypoxia-induced brain injuries in cynomolgus monkeys.

Hypobaric hypoxia (HH) exposure can cause serious brain injury as well as life-threatening cerebral edema in severe cases. Previous studies on the mechanisms of HH-induced brain injury have been conducted primarily using non-primate animal models that are genetically distant to humans, thus hindering the development of disease treatment. Here, we report that cynomolgus monkeys ( Macacafascicularis) exposed to acute HH developed human-like HH syndrome involving severe brain injury and abnormal behavior. Transcriptome profiling of white blood cells and brain tissue from monkeys exposed to increasing altitude revealed the central role of the HIF-1 and other novel signaling pathways, such as the vitamin D receptor (VDR) signaling pathway, in co-regulating HH-induced inflammation processes. We also observed profound transcriptomic alterations in brains after exposure to acute HH, including the activation of angiogenesis and impairment of aerobic respiration and protein folding processes, which likely underlie the pathological effects of HH-induced brain injury. Administration of progesterone (PROG) and steroid neuroprotectant 5α-androst-3ß,5,6ß-triol (TRIOL) significantly attenuated brain injuries and rescued the transcriptomic changes induced by acute HH. Functional investigation of the affected genes suggested that these two neuroprotectants protect the brain by targeting different pathways, with PROG enhancing erythropoiesis and TRIOL suppressing glutamate-induced excitotoxicity. Thus, this study advances our understanding of the pathology induced by acute HH and provides potential compounds for the development of neuroprotectant drugs for therapeutic treatment.

RES-Scanner: a software package for genome-wide identification of RNA-editing sites.

BACKGROUND: High-throughput sequencing (HTS) provides a powerful solution for the genome-wide identification of RNA-editing sites. However, it remains a great challenge to distinguish RNA-editing sites from genetic variants and technical artifacts caused by sequencing or read-mapping errors. RESULTS: Here we present RES-Scanner, a flexible and efficient software package that detects and annotates RNA-editing sites using matching RNA-seq and DNA-seq data from the same individuals or samples. RES-Scanner allows the use of both raw HTS reads and pre-aligned reads in BAM format as inputs. When inputs are HTS reads, RES-Scanner can invoke the BWA mapper to align reads to the reference genome automatically. To rigorously identify potential false positives resulting from genetic variants, we have equipped RES-Scanner with sophisticated statistical models to infer the reliability of homozygous genotypes called from DNA-seq data. These models are applicable to samples from either single individuals or a pool of multiple individuals if the ploidy information is known. In addition, RES-Scanner implements statistical tests to distinguish genuine RNA-editing sites from sequencing errors, and provides a series of sophisticated filtering options to remove false positives resulting from mapping errors. Finally, RES-Scanner can improve the completeness and accuracy of editing site identification when the data of multiple samples are available. CONCLUSION: RES-Scanner, as a software package written in the Perl programming language, provides a comprehensive solution that addresses read mapping, homozygous genotype calling, de novo RNA-editing site identification and annotation for any species with matching RNA-seq and DNA-seq data. The package is freely available.