An immune cell atlas reveals the dynamics of human macrophage specification during prenatal development.

Macrophages are heterogeneous and play critical roles in development and disease, but their diversity, function, and specification remain inadequately understood during human development. We generated a single-cell RNA sequencing map of the dynamics of human macrophage specification from PCW 4-26 across 19 tissues. We identified a microglia-like population and a proangiogenic population in 15 macrophage subtypes. Microglia-like cells, molecularly and morphologically similar to microglia in the CNS, are present in the fetal epidermis, testicle, and heart. They are the major immune population in the early epidermis, exhibit a polarized distribution along the dorsal-lateral-ventral axis, and interact with neural crest cells, modulating their differentiation along the melanocyte lineage. Through spatial and differentiation trajectory analysis, we also showed that proangiogenic macrophages are perivascular across fetal organs and likely yolk-sac-derived as microglia. Our study provides a comprehensive map of the heterogeneity and developmental dynamics of human macrophages and unravels their diverse functions during development.

The emerging role of mtDNA release in sepsis: Current evidence and potential therapeutic targets.

Sepsis is a systemic inflammatory reaction caused by infection, and severe sepsis can develop into septic shock, eventually leading to multiorgan dysfunction and even death. In recent years, studies have shown that mitochondrial damage is closely related to the occurrence and development of sepsis. Recent years have seen a surge in concern over mitochondrial DNA (mtDNA), as anomalies in this material can lead to cellular dysfunction, disruption of aerobic respiration, and even death of the cell. In this review, we discuss the latest findings on the mechanisms of mitochondrial damage and the molecular mechanisms controlling mitochondrial mtDNA release. We also explored the connection between mtDNA misplacement and inflammatory activation. Additionally, we propose potential therapeutic targets of mtDNA for sepsis treatment.

Activation of toll-like receptor 4/nuclear factor-kappa B signaling by triggering a receptor expressed on myeloid cells 1 promotes alveolar macrophage M1 polarization and exacerbates septic acute lung injury.

BACKGROUND: Septic acute lung injury (ALI) is a life-threatening condition commonly occurring in the intensive care unit. Inflammation is considered as the basic pathological response of septic ALI. Triggering receptor expressed on myeloid cells 1 (TREM1) is a member of the immunoglobulin superfamily receptors that regulates the inflammatory response. However, the role of TREM1 in septic ALI has not yet been reported. METHODS: Cell viability was tested using the MTT assay. TdT-mediated dUTP nick end labeling assay and flow cytometry were used for apoptosis. The level of protein was detected using western blot analysis. The levels of tumor necrosis factor-α and interleukin-1ß were assessed using enzyme-linked immunosorbent assay. The lactate dehydrogenase content was assessed using the assay kit. Myeloperoxidase activity was determined using an assay. Histology of lung tissue was further analyzed through hematoxylin-eosin staining. RESULTS: We found that TREM1 knockdown by transfection with si-TREM1 inhibited lipopolysaccharide (LPS)-induced cell apoptosis of alveolar macrophage cell line MH-S. The LPS stimulation caused M1 polarization of MH-S cells, which could be reversed by TREM1 knockdown. In vivo assays proved that si-TREM1 injection improved lung injury and inflammation of cecal ligation and puncture-induced ALI in mice. In addition, TREM1 knockdown suppressed the activation of toll-like receptor 4/nuclear factor-kappa B signaling, implying the involvement of TLR4 in the effects of TREM1 in response to LPS stimulation. CONCLUSIONS: This study examined the proinflammatory role of TREM1 in septic ALI and its regulatory effect on alveolar macrophage polarization. These results suggest that TREM1 could potentially serve as a therapeutic target in the prevention and treatment of ALI.

Optimization of Thermal Control Design for Aerial Reflective Opto-Mechanical Structure.

To improve the adaptability of aerial reflective opto-mechanical structures (mainly including the primary mirror and secondary mirror) to low-temperature environments, typically below -40 °C, an optimized thermal control design, which includes passive insulation and temperature-negative feedback-variable power zone active heating, is proposed. Firstly, the relationship between conventional heating methods and the axial/radial temperature differences of mirrors with different shapes is analyzed. Based on the heat transfer analyses, it is pointed out that optimized thermal control design is necessary to ensure the temperature uniformity of the fused silica mirror, taking into account the temperature level when the aerial electro-optics system is working in low-temperature environments. By adjusting the input voltage based on the measured temperature, the heating power of the subregion is changed accordingly, so as to locally increase or decrease the temperature of the mirrors. The thermal control scheme ensures that the average temperature of the mirror fluctuates slowly and slightly around 20 °C. At the same time, the temperature differences within a mirror and between the primary mirror and the secondary mirror can be controlled within 5 °C. Thereby, the resolution of EO decreases by no more than 11.4%.

Synergistic Interactions of Neighboring Platinum and Iron Atoms Enhance Reverse Water-Gas Shift Reaction Performance.

The limitations of conventional strategies in finely controlling the composition and structure demand new promotional effects for upgrading the reverse water-gas shift (RWGS) catalysts for enhanced fuel production. We report the design and synthesis of a hetero-dual-site catalyst for boosting RWGS performance by controllably loading Fe atoms at the neighboring Pt atom on the surface of commercial CeO2. The Fe-Pt/CeO2 exhibits a remarkably high catalytic performance (TOFPt: 43,519 h-1) for CO2 to CO conversion with ∼100% CO selectivity at a relatively low temperature of 350 °C. Furthermore, the catalyst retains over 80% activity after 200 h of continuous operation. The experimental and computational investigations reveal a "two-way synergistic effect", where Fe atoms can not only serve as promotors to alter the charge density of Pt atoms but also be activated by the excess active hydrogen species generated by Pt atoms, enhancing catalytic activity and stability.

Transcriptome and miRNAs Profiles Reveal Regulatory Network and Key Regulators of Secondary Xylem Formation in "84K" Poplar.

Secondary xylem produced by stem secondary growth is the main source of tree biomass and possesses great economic and ecological value in papermaking, construction, biofuels, and the global carbon cycle. The secondary xylem formation is a complex developmental process, and the underlying regulatory networks and potential mechanisms are still under exploration. In this study, using hybrid poplar (Populus alba × Populus glandulosa clone 84K) as a model system, we first ascertained three representative stages of stem secondary growth and then investigated the regulatory network of secondary xylem formation by joint analysis of transcriptome and miRNAs. Notably, 7507 differentially expressed genes (DEGs) and 55 differentially expressed miRNAs (DEMs) were identified from stage 1 without initiating secondary growth to stage 2 with just initiating secondary growth, which was much more than those identified from stage 2 to stage 3 with obvious secondary growth. DEGs encoding transcription factors and lignin biosynthetic enzymes and those associated with plant hormones were found to participate in the secondary xylem formation. MiRNA-target analysis revealed that a total of 85 DEMs were predicted to have 2948 putative targets. Among them, PagmiR396d-PagGRFs, PagmiR395c-PagGA2ox1/PagLHW/PagSULTR2/PagPolyubiquitin 1, PagmiR482d-PagLAC4, PagmiR167e-PagbHLH62, and PagmiR167f/g/h-PagbHLH110 modules were involved in the regulating cambial activity and its differentiation into secondary xylem, cell expansion, secondary cell wall deposition, and programmed cell death. Our results give new insights into the regulatory network and mechanism of secondary xylem formation.

ARG1 and CXCL2 are potential biomarkers target for psoriasis patients.

BACKGROUND: Psoriasis is a common chronic skin inflammatory disease. Understanding the pathogenesis of psoriasis and identifying novel therapeutic targets are under investigation. METHODS: Gene expression profiles were obtained from GSE13355, GSE30999 and GSE54456 datasets to identify differentially expressed genes (DEGs) between psoriasis and normal controls. Enrichment analysis was used to identify the biological functions and pathways of common genes from three groups of DEGs. Protein-protein interaction (PPI) network was then constructed to identify key genes according to degree of connectivity. Expression of genes was detected by the method of qRT-PCR and immunohistochemistry. The infiltration of immune cells of psoriasis were quantified and detected by flow cytometry. RESULTS: A total of 146 common genes were identified between psoriasis and normal controls. They were significantly enriched in IL-17, chemokine, and NOD-like receptor (NLR) signaling pathway. Ten key genes were selected with bigger degree of connectivity through PPI network, and ARG1 and CXCL2 had better predictive ability based on ROC curves. Increased expression of ARG1 and CXCL2 in psoriasis patients were verified by qRT-PCR and immunohistochemistry method. In addition, a lot of immune cells were upregulated in psoriasis compared to healthy controls through ssGSEA and flow cytometry. CONCLUSION: ARG1 and CXCL2 may serve as biomarkers and potential therapy for psoriasis. This may be related to the immune response and NLR pathway.

Genome Sequencing Explores Complexity of Chromosomal Abnormalities in Recurrent Miscarriage.

Recurrent miscarriage (RM) affects millions of couples globally, and half of them have no demonstrated etiology. Genome sequencing (GS) is an enhanced and novel cytogenetic tool to define the contribution of chromosomal abnormalities in human diseases. In this study we evaluated its utility in RM-affected couples. We performed low-pass GS retrospectively for 1,090 RM-affected couples, all of whom had routine chromosome analysis. A customized sequencing and interpretation pipeline was developed to identify chromosomal rearrangements and deletions/duplications with confirmation by fluorescence in situ hybridization, chromosomal microarray analysis, and PCR studies. Low-pass GS yielded results in 1,077 of 1,090 couples (98.8%) and detected 127 chromosomal abnormalities in 11.7% (126/1,077) of couples; both members of one couple were identified with inversions. Of the 126 couples, 39.7% (50/126) had received former diagnostic results by karyotyping characteristic of normal human male or female karyotypes. Low-pass GS revealed additional chromosomal abnormalities in 50 (4.0%) couples, including eight with balanced translocations and 42 inversions. Follow-up studies of these couples showed a higher miscarriage/fetal-anomaly rate of 5/10 (50%) compared to 21/93 (22.6%) in couples with normal GS, resulting in a relative risk of 2.2 (95% confidence interval, 1.1 to 4.6). In these couples, this protocol significantly increased the diagnostic yield of chromosomal abnormalities per couple (11.7%) in comparison to chromosome analysis (8.0%, chi-square test p = 0.000751). In summary, low-pass GS identified underlying chromosomal aberrations in 1 in 9 RM-affected couples, enabling identification of a subgroup of couples with increased risk of subsequent miscarriage who would benefit from a personalized intervention.

Caproicibacterium lactatifermentans sp. nov., isolated from pit clay used for the production of Chinese strong aroma-type liquor.

Two recently reported bacterial strains that were identified as the dominant caproate-producing bacteria in pit clay, were further characterized to determine their phylogeny and taxonomy. The two strains, designated as LBM19010T and JNU-WLY1368, were short rod-shaped, Gram-stain-positive, non-motile and strictly anaerobic. Analysis of the 16S rRNA gene sequences revealed that strains LBM19010T and JNU-WLY1368 shared a 16S rRNA gene sequence similarity of 99.93 % and belonged to a recent proposed genus Caproicibacterium in the family Oscillospiraceae. The proposed type strain, LBM19010T, showed the highest 16S rRNA gene sequence similarity to Caproicibacterium amylolyticum LBM18003T (96.34%), followed by Caproiciproducens galactitolivorans JCM 30532T (94.14 %). The pairwise average nucleotide identity and average amino acid identity values between strains LBM19010T and LBM18003T were 74.84 and 76.18 %, respectively. Growth of strain LBM19010T occurred at pH 4.5-7.5 (optimum, pH 5.0-5.5), 20-40 °C (optimum, 35 °C) and with 0-1 % (w/v) NaCl (optimum, 0 %). Strains LBM19010T and JNU-WLY1368 were both able to ferment several hexoses, disaccharides, starch and lactate but not pentoses. Caproate and butyrate were the major end-products from glucose. The predominant cellular fatty acids (>10 %) of strain LBM19010T were C16 : 0 (56.3 %), C14 : 0 DMA (19.5 %) and C14 : 0 (14.9 %). The identified polar lipids of strain LBM19010T were diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids and nine unidentified glycolipids. Based on phylogenetic, phenotypic and chemotaxonomic evidence, strains LBM19010T and JNU-WLY1368 belong to a novel species of the genus Caproicibacterium, for which the name Caproicibacterium lactatifermentans sp. nov. is proposed. The type strain is LBM19010T (=GDMCC 1.1627T=JCM 33782T).

Proteiniphilum propionicum sp. nov., a novel member of the phylum Bacteroidota isolated from pit clay used to produce Chinese liquor.

A novel, Gram-stain-negative, rod-shaped, strictly anaerobic bacterium of genus Proteiniphilum of the phylum Bacteroidota, named strain JNU-WLY501T, was isolated from pit clay used to produce strong aroma-type liquor in PR China. The genomic DNA G+C content and genome size of JNU-WLY501T were 41.4 % and 3.9 Mbp, respectively. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that JNU-WLY501T was closely related to Proteiniphilum acetatigenes DSM 18083T (95.7 %) and Proteiniphilum saccharofermentans M3/6T (94.9 %). The pairwise average nucleotide identity based on blast and average amino acid identity values of JNU-WLY501T compared with Proteiniphilum saccharofermentans M3/6T were 73.6 and 77.3 %, respectively, which both were lower than the threshold values for bacterial species delineation. The strain grew at 20-40 °C, with optimum growth at 37 °C. The pH range for growth was 5.4-9.1, with optimum growth at pH 7.5. The sodium chloride range for growth was 0.0-4.0 %, with optimum growth at 0 %. The strain did not use glucose, maltose, fructose or starch. Yeast extract, tryptone and peptone supported the growth of JNU-WLY501T, and the main fermentation products were acetate and propionate. The predominant cellular fatty acids (>5 %) of JNU-WLY501T were anteiso-C15 : 0 (30.6 %), anteiso-C17 : 0 (26.1 %), C16 : 0 (7.7 %), iso-C16 : 0 (5.0 %) and iso-C17 : 0 (5.0 %). The respiratory quinone of JNU-WLY501T was MK-5. On the basis of the morphological, physiological, biochemical, chemotaxonomic, genotypic and phylogenetic results, JNU-WLY501T represents a novel species of the genus Proteiniphilum, for which the name Proteiniphilum propionicum sp. nov. is proposed. The type strain is JNU-WLY501T (=GDMCC 1.2686T=JCM 34753T).

Crystal structure of the polyketide cyclase from Mycobacterium tuberculosis.

About 40% of proteins are classified as conserved hypothetical proteins in Mycobacterium tuberculosis (TB). Identification and characterization of these proteins are beneficial to understand the pathogenesis of TB and exploiting novel drugs for TB treatments. The polyketide cyclase, a protein from M. tuberculosis ( MtPC) has been annotated as a hypothetical protein in Uniprot database. Sequence analysis shows that the MtPC belongs to the NTF2-like superfamily proteins with diverse functions. Here, we determined the crystal structure of MtPC at a resolution of 2.4 Šand measured backbone relaxation parameters for the MtPC protein. MtPC exists as a dimer in solution, and each subunit contains a six-stranded mixed ß-sheet and three α helixes which are arranged in the order α1-α2-ß1-ß2-α3-ß3-ß4-ß5-ß6. The NMR dynamics analysis showed that the overall structure of MtPC is highly rigid on ps-ns time scales. Furthermore, we predicted the potential function of MtPC based on the crystal structure. Our results lay the basis for further exploiting and mechanistically understanding the biological functions of MtPC.

Downregulation of the CsABCC2 gene is associated with Cry1C resistance in the striped stem borer Chilo suppressalis.

Chilo suppressalis is a major target pest of transgenic rice expressing the Bacillus thuringiensis (Bt) Cry1C toxin in China. The evolution of resistance of this pest is a major threat to Bt rice. Since Bt functions by binding to receptors in the midgut (MG) of target insects, identification of Bt functional receptors in C. suppressalis is crucial for evaluating potential resistance mechanisms and developing effective management strategies. ATP-binding cassette (ABC) transporters have been vastly reported to interact with Cry1A toxins, as receptors and their mutations cause insect Bt resistance. However, the role of ABC transporters in Cry1C resistance to C. suppressalis remains unknown. Here, we measured CsABCC2 expression in C. suppressalis Cry1C-resistant (Cry1C-R) and Cry1C-susceptible strains (selected in the laboratory) via quantitative real-time PCR (qRT-PCR); the transcript level of CsABCC2 in the Cry1C-R strain was significantly lower than that in the Cry1C-susceptible strain. Furthermore, silencing CsABCC2 in C. suppressalis via RNA interference (RNAi) significantly decreased Cry1C susceptibility. Overall, CsABCC2 participates in Cry1C mode of action, and reduced expression of CsABCC2 is functionally associated with Cry1C resistance in C. suppressalis.

The Regulation of Xylem Development by Transcription Factors and Their Upstream MicroRNAs.

Xylem, as a unique organizational structure of vascular plants, bears water transport and supports functions necessary for plant survival. Notably, secondary xylem in the stem (i.e., wood) also has important economic and ecological value. In view of this, the regulation of xylem development has been widely concerned. In recent years, studies on model plants Arabidopsis and poplar have shown that transcription factors play important regulatory roles in various processes of xylem development, including the directional differentiation of procambium and cambium into xylem, xylem arrangement patterns, secondary cell wall formation and programmed cell death. This review focuses on the regulatory roles of widely and thoroughly studied HD-ZIP, MYB and NAC transcription factor gene families in xylem development, and it also pays attention to the regulation of their upstream microRNAs. In addition, the existing questions in the research and future research directions are prospected.

Adaptability of a Caproate-Producing Bacterium Contributes to Its Dominance in an Anaerobic Fermentation System.

The transformation of diverse feedstocks into medium-chain fatty acids (MCFAs) by mixed cultures is a promising biorefinery route because of the high value of MCFAs. A particular concern is how to maintain the microbial consortia in mixed cultures to achieve stable MCFA production. The Chinese strong aroma-type liquor (Baijiu) fermentation system continually produces caproic acid for decades through a spontaneous inoculation of anaerobes from pit mud into fermented grains. Therefore, illuminating the dominant caproate-producing bacterium (CPB) in pit mud and how the CPB is sustained in the spontaneous fermentation system will help to reveal the microbiological mechanisms of stable caproate production. Here, we examined pit mud samples across four Chinese strong aroma-type Baijiu-producing areas and found that a caproate-producing Caproicibacterium sp. was widely distributed in these distilleries, with relative abundance ranging from 1.4 to 35.5% and an average abundance of 11.4%. Through controlling carbon source availability, we obtained different simplified caproate-producing consortia and found that the growth advantage of Caproicibacterium sp. was highly dependent on glucose. Then, two strains, named Caproicibacterium sp. strain LBM19010 and Caproicibacterium sp. strain JNU-WLY1368, were isolated from pit mud of two regions. The metabolic versatility of this species utilizing starch, maltose, glucose, and lactate reflected its adaptability to the fermentation environment where these carbon sources coexist. The simultaneous utilization of glucose and lactate contributed to the balance between cell growth and pH homeostasis. This study reveals that multiple adaptation strategies employed by the predominant CPB promotes its stability and dominance in a saccharide- and lactate-rich anaerobic habitat. IMPORTANCE The Chinese strong aroma-type liquor (Baijiu) fermentation environment is a typical medium-chain fatty acid-producing system with complex nutrients. Although several studies have revealed the correlation between microbial community composition and abiotic factors, the adaptation mechanisms of dominant species to abiotic environment are still unknown in this special anaerobic habitat. This study identified the predominant CPB in Chinese strong aroma-type Baijiu fermentation system. Metabolic versatility and flexibility of the dominant CPB with a small-size genome indicated that this bacterium can effectively exploit available carbon and nitrogen sources, which could be a key factor to promote its ecological success in a multispecies environment. The understanding of growth and metabolic features of the CPB responsible for its dominance in microbial community will not only contribute to the improvement of Chinese strong aroma-type Baijiu production but also expand its potential industrial applications in caproate production.

Network analysis of potential risk genes for psoriasis.

BACKGROUND: Psoriasis is a complex chronic inflammatory skin disease. The aim of this study was to analyze potential risk genes and molecular mechanisms associated with psoriasis. METHODS: GSE54456, GSE114286, and GSE121212 were collected from gene expression omnibus (GEO) database. Differentially expressed genes (DEGs) between psoriasis and controls were screened respectively in three datasets and common DEGs were obtained. The biological role of common DEGs were identified by enrichment analysis. Hub genes were identified using protein-protein interaction (PPI) networks and their risk for psoriasis was evaluated through logistic regression analysis. Moreover, differentially methylated positions (DMPs) between psoriasis and controls were obtained in the GSE115797 dataset. Methylation markers were identified after comparison with the common genes. RESULTS: A total of 118 common DEGs were identified, which were mainly involved in keratinocyte differentiation and IL-17 signaling pathway. Through PPI network, we identified top 10 degrees as hub genes. Among them, high expression of CXCL9 and SPRR1B may be risk factors for psoriasis. In addition, we selected 10 methylation-modified genes with the higher area under receiver operating characteristic curve (AUC) value as methylation markers. Nomogram showed that TGM6 and S100A9 may be associated with an increased risk of psoriasis. CONCLUSION: This suggests that immune and inflammatory responses are active in keratinocytes of psoriatic skin. CXCL9, SPRR1B, TGM6 and S100A9 may be potential targets for the diagnosis and treatment of psoriasis.

Ghrelin inhibits IKKß/NF-κB activation and reduces pro-inflammatory cytokine production in pancreatic acinar AR42J cells treated with cerulein.

BACKGROUND: Previous studies have provided conflicting results regarding whether the serum ghrelin concentration can reflect the severity of acute pancreatitis (AP). The present study examined the correlation between the serum ghrelin concentration and AP severity in animal models and investigated whether altered ghrelin expression in pancreatic acinar cells influences IKKß/NF-κB signaling and pro-inflammatory cytokine production. METHODS: Mild or severe AP was induced in rats by intraperitoneal injection of cerulein or retrograde cholangiopancreatic duct injection of sodium taurocholate, respectively. After successful model induction, serum ghrelin, tumor necrosis factor-α (TNF-α), and interleukin-6 (IL-6) concentrations were determined by enzyme-linked immunosorbent assay, and IKKß/NF-κB activation was assessed by immunohistochemistry. Subsequently, stable overexpression or knockdown of ghrelin in AR42J cells was achieved by lentiviral transfection. After transfected cells and control cells were treated with cerulein for 24 h, the TNF-α and IL-1ß levels in the supernatants were determined by enzyme-linked immunosorbent assay, and the expression levels of p-p65, IKKß, and p-IKKß were detected by Western blotting. RESULTS: In rat AP models, AP severity was correlated with increased IKKß/NF-κB activation, pro-inflammatory cytokine production, and ghrelin secretion. The levels of pro-inflammatory cytokines TNF-α and IL-1ß as well as IKKß/NF-κB signaling activity were increased upon knockdown of ghrelin in the AP acinar cell model and decreased with ghrelin overexpression. CONCLUSIONS: Serum ghrelin is related to the severity of AP. Ghrelin may play a protective role in the pathogenesis of AP by inhibiting the pro-inflammatory cytokines and the activation of the IKKß/NF-κB signaling pathway.

Ball-Milling Induced Debonding of Surface Atoms from Metal Bulk for Construing High-Performance Dual-Site Single-Atom Catalysts.

One of the most pressing challenges in single-atom catalysis is the manipulation of the coordination environment of central metals to maximize the catalyst performance. Herein, we fabricated a high-performance catalyst (Co-SNC) by introducing S into the neighboring position of the Co-N4 coordination. The developed ball-milling method enabled large-scale synthesis, that over 4.7 g of Co-SNC can be produced in one pot. In benzylamine coupling reaction, Co-SNC exhibited the highest conversion of 97.5 % with 99 % selectivity toward N-benzylidenebenzylamine in 10 h among various Co catalysts. Density functional theory calculations revealed the crucial role of S atoms, which serve as the active sites for O2 activation, leaving the Co atoms free to adsorb benzylamine. Consequently, the adsorption energies of O2 and benzylamine were significantly increased. Our strategy suggests a feasible approach to enhance catalytic performance by delicately integrating dual active sites into a single catalyst unit.

Low-pass genome sequencing: a validated method in clinical cytogenetics.

Clinically significant copy-number variants (CNVs) known to cause human diseases are routinely detected by chromosomal microarray analysis (CMA). Recently, genome sequencing (GS) has been introduced for CNV analysis; however, sequencing depth (determined by sequencing read-length and read-amount) is a variable parameter across different laboratories. Variating sequencing depths affect the CNV detection resolution and also make it difficult for cross-laboratory referencing or comparison. In this study, by using data from 50 samples with high read-depth GS (30×) and the reported clinically significant CNVs, we first demonstrated the optimal read-amount and the most cost-effective read-length for CNV analysis to be 15 million reads and single-end 50 bp (equivalent to a read-depth of 0.25-fold), respectively. In addition, we showed that CNVs at mosaic levels as low as 30% are readily detected, furthermore, CNVs larger than 2.5 Mb are also detectable at mosaic levels as low as 20%. Herein, by conducting a retrospective back-to-back comparison study of low-pass GS versus routine CMA for 532 prenatal, miscarriage, and postnatal cases, the overall diagnostic yield was 22.4% (119/532) for CMA and 23.1% (123/532) for low-pass GS. Thus, the overall relative improvement of the diagnostic yield by low-pass GS versus CMA was ~ 3.4% (4/119). Identification of cryptic and clinically significant CNVs among prenatal, miscarriage, and postnatal cases demonstrated that CNV detection at higher resolutions is warranted for clinical diagnosis regardless of referral indications. Overall, our study supports low-pass GS as the first-tier genetic test for molecular cytogenetic testing.

Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity.

X-ray crystallography is the main tool for structural determination of proteins. Yet, the underlying crystallization process is costly, has a high attrition rate and involves a series of trial-and-error attempts to obtain diffraction-quality crystals. The Structural Genomics Consortium aims to systematically solve representative structures of major protein-fold classes using primarily high-throughput X-ray crystallography. The attrition rate of these efforts can be improved by selection of proteins that are potentially easier to be crystallized. In this context, bioinformatics approaches have been developed to predict crystallization propensities based on protein sequences. These approaches are used to facilitate prioritization of the most promising target proteins, search for alternative structural orthologues of the target proteins and suggest designs of constructs capable of potentially enhancing the likelihood of successful crystallization. We reviewed and compared nine predictors of protein crystallization propensity. Moreover, we demonstrated that integrating selected outputs from multiple predictors as candidate input features to build the predictive model results in a significantly higher predictive performance when compared to using these predictors individually. Furthermore, we also introduced a new and accurate predictor of protein crystallization propensity, Crysf, which uses functional features extracted from UniProt as inputs. This comprehensive review will assist structural biologists in selecting the most appropriate predictor, and is also beneficial for bioinformaticians to develop a new generation of predictive algorithms.

Low-pass genome sequencing versus chromosomal microarray analysis: implementation in prenatal diagnosis.

PURPOSE: Emerging studies suggest that low-pass genome sequencing (GS) provides additional diagnostic yield of clinically significant copy-number variants (CNVs) compared with chromosomal microarray analysis (CMA). However, a prospective back-to-back comparison evaluating accuracy, efficacy, and incremental yield of low-pass GS compared with CMA is warranted. METHODS: A total of 1023 women undergoing prenatal diagnosis were enrolled. Each sample was subjected to low-pass GS and CMA for CNV analysis in parallel. CNVs were classified according to guidelines of the American College of Medical Genetics and Genomics. RESULTS: Low-pass GS not only identified all 124 numerical disorders or pathogenic or likely pathogenic (P/LP) CNVs detected by CMA in 121 cases (11.8%, 121/1023), but also defined 17 additional and clinically relevant P/LP CNVs in 17 cases (1.7%, 17/1023). In addition, low-pass GS significantly reduced the technical repeat rate from 4.6% (47/1023) for CMA to 0.5% (5/1023) and required less DNA (50 ng) as input. CONCLUSION: In the context of prenatal diagnosis, low-pass GS identified additional and clinically significant information with enhanced resolution and increased sensitivity of detecting mosaicism as compared with the CMA platform used. This study provides strong evidence for applying low-pass GS as an alternative prenatal diagnostic test.