[Clinical features and genetic analysis of 17 Chinese pedigrees affected with X-linked intellectual disability].

OBJECTIVE: To analyze the clinical features and genetic etiology of 17 Chinese pedigrees affected with X-linked intellectual disability (XLID). METHODS: Seventeen pedigrees affected with unexplained intellectual disability which had presented at Henan Provincial People's Hospital from May 2021 to May 2023 were selected as the study subjects. Clinical data of the probands and their pedigree members were collected. Trio-whole exome sequencing (Trio-WES), Sanger sequencing and X chromosome inactivation (XCI) analysis were carried out. Pathogenicity of candidate variants was predicted based on the guidelines from the American College of Medical Genetics and Genomics and co-segregation analysis. RESULTS: The 17 probands, including 9 males and 8 females with an age ranging from 0.6 to 8 years old, had all shown mental retardation and developmental delay. Fourteen variants were detected by genetic testing, which included 4 pathogenic variants (MECP2: c.502C>T, MECP2: c.916C>T/c.806delG, IQSEC2: c.1417G>T), 4 likely pathogenic variants (MECP2: c.1157_1197del/c.925C>T, KDM5C: c.2128A>T, SLC6A8: c.1631C>T) and 6 variants of uncertain significance (KLHL15: c.26G>C, PAK3: c.970A>G/c.1520G>A, GRIA3: c.2153C>G, TAF1: c.2233T>G, HUWE1: c.10301T>A). The PAK3: c.970A>G, GRIA3: c.2153C>G and TAF1: c.2233T>G variants were considered as the genetic etiology for pedigrees 12, 14 and 15 by co-segregation analysis, respectively. The proband of pedigree 13 was found to have non-random XCI (81:19). Therefore, the PAK3: c.1520G>A variant may underlie its pathogenesis. CONCLUSION: Trio-WES has attained genetic diagnosis for the 17 XLID pedigrees. Sanger sequencing and XCI assay can provide auxiliary tests for the diagnosis of XLID.

Two-Dimensional Lanthanide Metal-Organic Frameworks as a Platform for Sensing Pollutant and Nitrophenols Reduction.

The discharge of harmful and toxic pollutants in water is destroying the ecosystem balance and human being health at an alarming rate. Therefore, the detection and removal of water pollutants by using stable and efficient materials are significant but challenging. Herein, three novel lanthanide metal-organic frameworks (Ln-MOFs), [La(L)(DMF)2(H2O)2]·H2O (LCUH-104), [Nd(L)(DMF)2(H2O)2]·H2O (LCUH-105), and [Pr(L)(DMF)2(H2O)2]·H2O (LCUH-106) [H3L = 5-(4-(tetrazol-5-yl)phenyl)isophthalic acid (H3TZI)] were solvothermally constructed and structurally characterized. In the three Ln-MOFs, dinuclear metallic clusters {Ln2} were connected by deprotonated tetrazol-containing dicarboxylate TZI3- to obtain a 2D layered framework with a point symbol of {42·84}·{46}. Their excellent chemical and thermal stabilities were beneficial to carry out fluorescence sensing and achieve the catalytic nitrophenols (NPs) reduction. Especially, the incorporation of the nitrogen-rich tetrazole ring into their 2D layered frameworks enables the fabrication of Pd nanocatalysts (Pd NPs@LCUH-104/105/106) and have dramatically enhanced catalytic activity by using the unique metal-support interactions between three Ln-MOFs and the encapsulating palladium nanoparticles (Pd NPs). Specifically, the reduction of NPs (2-NP, 3-NP, and 4-NP) in aqueous solution by Pd NPs@LCUH-104 exhibits exceptional conversion efficiency, remarkable rate constants (k), and outstanding cycling stability. The catalytic rate of Pd NPs@LCUH-104 for 4-NP is nearly 8.5 times more than that of Pd/C (wt 5%) and its turnover frequency value is 0.051 s-1, which indicate its excellent catalytic activity. Meanwhile, LCUH-105, as a multifunctional fluorescence sensor, exhibited excellent fluorescence detection of norfloxacin (NFX) (turn on) and Cr2O72- (turn off) with high selectivity and sensitivity at a low concentration, and the corresponding fluorescence enhancement/quenching mechanism has also been systematically investigated through various detection means and theoretical calculations.

A Multifunctional Co-Based Metal-Organic Framework as a Platform for Proton Conduction and Ni trophenols Reduction.

The design and development of proton conduction materials for clean energy-related applications is obviously important and highly desired but challenging. An ultrastable cobalt-based metal-organic framework Co-MOF, formulated as [Co2(btzip)2(µ2-OH2)] (namely, LCUH-103, H2btzip = 4, 6-bis(triazol-1-yl)-isophthalic acid) had been successfully synthesized via the hydrothermal method. LCUH-103 exhibits a three-dimensional framework and a one-dimensional microporous channel structure with scu topology based on the binuclear metallic cluster {Co2}. LCUH-103 indicated excellent chemical and thermal stability; peculiarly, it can retain its entire framework in acid and alkali solutions with different pH values for 24 h. The excellent stability is a prerequisite for studying its proton conductivity, and its proton conductivity σ can reach up to 1.25 × 10-3 S·cm-1 at 80 °C and 100% relative humidity (RH). In order to enhance its proton conductivity, the proton-conducting material Im@LCUH-103 had been prepared by encapsulating imidazole molecules into the channels of LCUH-103. Im@LCUH-103 indicated an excellent proton conductivity of 3.18 × 10-2 S·cm-1 at 80 °C and 100% RH, which is 1 order of magnitude higher than that of original LCUH-103. The proton conduction mechanism was systematically studied by various detection means and theoretical calculations. Meanwhile, LCUH-103 is also an excellent carrier for palladium nanoparticles (Pd NPs) via a wetness impregnation strategy, and the nitrophenols (4/3/2-NP) reduction in aqueous solution by Pd@LCUH-103 indicated an outstanding conversion efficiency, high rate constant (k), and exceptional cycling stability. Specifically, the k value of 4-NP reduction by Pd@LCUH-103 is superior to many other reported catalysts, and its k value is as high as 1.34 min-1 and the cycling stability can reach up to 6 cycles. Notably, its turnover frequency (TOF) value is nearly 196.88 times more than that of Pd/C (wt 5%) in the reaction, indicating its excellent stability and catalytic activity.

Series of Dual Functional Two-Dimensional RE-OFs for Nitrophenol Reduction and Dye Separation.

The rational design and preparation of stable and multifunctional metal-organic frameworks (MOFs) with excellent catalysis and adsorption properties are desirable but are great challenges. The nitrophenol (NP) reduction to aminophenols (APs) by using the catalyst Pd@MOFs is an effective strategy, which has attracted extensive attention in recent years. Here, we report four stable isostructural two-dimensional (2D) rare earth metal-organic frameworks [RE4(AAPA)6(DMA)2 (H2O)4][DMA]3[H2O]8 (namely LCUH-101, RE = Eu, Gd, Tb, Y; AAPA2- = 5-[(anthracen-9-yl-methyl)-amino]-1,3-isophthalate), which feature a 2D layer structure with sql topology of point symbol {44·62} and exhibit excellent chemical stability and thermostability. The as-synthesized Pd@LCUH-101 was utilized for the catalytic reduction of 2/3/4-nitrophenol, which indicates high catalytic activity and recyclability attributed to the synergistic effect between Pd nanoparticles and the 2D layered structure. Of note, the turnover frequency (TOF), the reaction rate constant (k), and the activation energy (Ea) of Pd@LCUH-101 (Eu) in the reduction of 4-NP, respectively, are 1.09 s-1, 2.17 min-1, and 50.2 kJ·mol-1, which show that it has superior catalytic activity. Remarkably, LCUH-101 (Eu, Gd, Tb, and Y) are multifunctional MOFs that can effectively absorb and separate mixed dyes. The appropriate interlayer spacing enables them to efficiently adsorb methylene blue (MB) and rhodamine B (RhB) in aqueous solution, with adsorption capacities of 0.97 and 0.41 g·g-1, respectively, which is one of the highest values among those of the reported MOF-based adsorbers. Meanwhile, LCUH-101 (Eu) can be used for the separation of the dye mixture MB/MO and RhB/MO, and the excellent reusability enables LCUH-101 (Eu) to be used as chromatographic column filters to quickly separate and recover dyes. Therefore, this work provides a new strategy for the exploitation of stable and efficient catalysts for NP reduction and adsorbents for dyes.

Six Sets of Aromatic Polyketides Differing in Size and Shape Derive from a Single Biosynthetic Gene Cluster.

One new aromatic polyketide, prealnumycin B (1), and four known aromatic polyketides, K1115A (2), 1,6-dihydroxy-8-propylanthraquinone (DHPA, 3), phaeochromycin B (4), and (R)-7-acetyl-3,6-dihydroxy-8-propyl-3,4dihydronaphthalen-1(2H)-one (5), were isolated from the marine-derived Streptomyces sundarbansensis SCSIO NS01; these compounds represent four sets of aromatic polyketides differing in size and shape. A type II polyketide synthase (PKS) cluster, als, was identified by complete genome sequencing and was shown, by in vivo gene inactivation experiments in the wild-type (WT) NS01 strain and heterologous expression experiments, to encode the biosynthesis of compounds 1-5. Moreover, heterologous expression of the als cluster afforded three additional aromatic polyketides representing two different carbon skeletons, the new phaeochromycin L (6) and two known aromatic polyketides, phaeochromycins D (7) and E (8). These findings expand our knowledge of type II PKS machineries and their versatility in generating structurally diverse aromatic polyketides and highlight the power of type II PKSs in accessing new polyketides via ectopic expression in heterologous hosts.

Functionalized 2D defect g-C3N4 for artificial photosynthesis of H2O2 and synchronizing tetracycline fluorescence detection and degradation.

Artificial photosynthesis of H2O2 is a clean production technology, which brings the synergistic effect to photodegradation of pollutants. Inspired by defect engineering, 2D defective carbon nitride (g-C3N4) photocatalyst was obtained via potassium ion assisted synthesis. Defective g-C3N4 is protonated and applied to photosynthesis of H2O2, H2O2 concentration produced reached 477.7 µM, which was approximately 5.27 times that by pristine g-C3N4. Additionally, defective g-C3N4 materials are borrowed to synchronizing tetracycline (TC) fluorescence detection and degradation, suggesting the catalyst existed bifunctional characteristics of TC detection and degradation. Meanwhile, metal impregnation engineering (molybdenum) was borrowed enhancing the electron-trapping ability in local region of defective g-C3N4, which takes advantages to the efficient degradation of TC. Furthermore, optical and electrical properties of photocatalysts were investigated in details by advanced material characterization testing. This work provides potential applications in the field of artificial photosynthesis and pollution degradation.

Series of Stable Anionic Lanthanide Metal-Organic Frameworks as a Platform for Pollutant Separation and Efficient Nanoparticle Catalysis.

Eight new stable porous lanthanide metal-organic frameworks (Ln-OFs), namely, [Ln2(BPTC)2][(CH3)2NH2]2 [Ln = Ho (1), Eu (2), Gd (3), Dy (4), Er (5), Tm (6), Yb (7), Lu (8)], were prepared by 3,3',5,5'-biphenyltetracarboxylic acid (H4BPTC) and lanthanide ions by solvothermal reactions. Complexes 1-8 show a three-dimensional (3D) 6,6-connected network {412·63}·{48·66·8} topology based on binuclear (Ln2) clusters and feature a one-dimensional curving porous channel occupied by exchangeable dimethylamine cations ([(CH3)2NH2]+) in the 3D anionic frameworks. The occupied [(CH3)2NH2]+ in the anionic channels exhibited excellent ion-exchange ability, which is favorable to Pd2+ and cationic dye adsorption. Consequently, 1-8 were used to load Pd nanoparticles to catalyze the reduction of nitrophenols and adsorb and desorb methyl blue (MB). The catalytic reaction efficiencies of Pd@1-8 were higher than that of Pd/C (5 wt %) in the hydrogenation reaction of p-nitrophenol (p-NP). Moreover, Pd@1 exhibited good cycle stability and achieved nearly 100% p-NP conversion after eight cycles. Meanwhile, compound 1 also exhibited a high adsorption ability of MB, possessing an adsorption capacity of 1.41 g·g-1 (second only to 1.49 g·g-1 reported in the literature) selectively over rhodamine B (RhB) and methyl orange (MO) in aqueous solutions. Remarkably, the skeleton of 1 remained stable after four adsorption-desorption cycles of MB in aqueous solution.

Series of TM-OFs as a Platform for Efficient Catalysis and Multifunctional Luminescence Sensing.

Three novel porous transition-metal-organic frameworks (TM-OFs), formulated as [Co3(DCPN)2(µ2-OH2)4(H2O)4](DMF)2 (1), [Cd3(DCPN)2(µ2-OH2)4(H2O)4](DMF)2 (2), and [CdK(DCPN)(DMA)] (3), have been successfully prepared via solvothermal conditions based on a 5-(3',6'-dicarboxylic phenyl) nicotinic carboxylic acid (H3DCPN) ligand. 1 and 2 both have the same porous 3D network structure with the point symbol of {410·614·84}·{45·6}2 based on trinuclear ({Co3} or {Cd3}) clusters, indicating a one-dimensional porous channel, and possess excellent water and thermal stability; 3 also displays a porous 3D network structure with a 4-connected sra topology based on the heteronuclear metal cluster {CdK}. Complex 1 can be used to load Pd nanoparticles (Pd NPs) via a wetness impregnation strategy to obtain Pd@1. The reduction of nitrophenols (2-NP, 3-NP, 4-NP) by Pd@1 in aqueous solution shows outstanding conversion, excellent rate constants (k), and remarkable cycling stability due to the synergistic effect of complex 1 and Pd NPs. Luminescence sensing tests confirmed that 2 is a reliable multifunctional chemical sensor with high selectivity and sensitivity for low concentrations of Fe3+, Cr2O72-, CPFX, and NFX. Specifically, 2 shows a fluorescence enhancement behavior toward fluoroquinolone antibiotics (CPFX and NFX), which has not been reported previously in the literature. Moreover, the rational mechanism of fluorescence sensing was also systematically investigated by various detection means and theoretical calculations.

Halo- and Thiocarbazomycins from Coral- and Coral Reef Sands-Derived Actinomycetes.

Four actinomycete strains isolated from the coral Acropora austera and coral sand samples from the South China Sea, were found to produce a series of halogenated compounds baring similar ultraviolet absorption based on the analysis of HPLC and LC-MS. The production titers of halogenated compounds from Streptomyces diacarni SCSIO 64983 exceeded those of other similar strains leading us to focus on SCSIO 64983. Four new thiocarbazomycins A-B (1-2), chlocarbazomycin E (3), and brocarbazomycin A (4), together with three known chlocarbazomycins A-C (5-7) containing a carbazole core were identified, and their structures were determined using a combination of spectroscopic analysis including HRESIMS, 1D and 2D NMR. Structurally speaking, compounds 1 and 2 have the rare sulfur-containing carbazole nuclei, and 3 and 4 contain Cl and Br atoms, respectively. Although these compounds have not yet been found to have obvious biological activity, their discovery highlights the role of molecular libraries in subsequent drug discovery campaigns.

Bacterial Quorum-Sensing Signal DSF Inhibits LPS-Induced Inflammations by Suppressing Toll-like Receptor Signaling and Preventing Lysosome-Mediated Apoptosis in Zebrafish.

Bacteria and their eukaryotic hosts have co-evolved for millions of years, and the former can intercept eukaryotic signaling systems for the successful colonization of the host. The diffusible signal factor (DSF) family represents a type of quorum-sensing signals found in diverse Gram-negative bacterial pathogens. Recent evidence shows that the DSF is involved in interkingdom communications between the bacterial pathogen and the host plant. In this study, we explored the anti-inflammatory effect of the DSF and its underlying molecular mechanism in a zebrafish model. We found that the DSF treatment exhibited a strong protective effect on the inflammatory response of zebrafish induced by lipopolysaccharide (LPS). In the LPS-induced inflammation zebrafish model, the DSF could significantly ameliorate the intestinal pathological injury, reduce abnormal migration and the aggregation of inflammatory cells, inhibit the excessive production of inflammatory mediator reactive oxygen species (ROS) content, and prevent apoptosis. Through an RNA-Seq analysis, a total of 938 differentially expressed genes (DEGs) was screened between LPS and LPS + DSF treatment zebrafish embryos. A further bioinformatics analysis and validation revealed that the DSF might inhibit the LPS-induced zebrafish inflammatory response by preventing the activation of signaling in the Toll-like receptor pathway, attenuating the expression of pro-inflammatory cytokines and chemokines, and regulating the activation of the caspase cascade through restoring the expression of lysosomal cathepsins and apoptosis signaling. This study, for the first time, demonstrates the anti-inflammatory role and a potential pharmaceutical application of the bacterial signal DSF. These findings also suggest that the interkingdom communication between DSF-producing bacteria and zebrafish might occur in nature.

Efficacy and Safety of Dupilumab in Glucocorticoid-Dependent Severe Asthma.

BACKGROUND: Dupilumab is a fully human anti-interleukin-4 receptor α monoclonal antibody that blocks both interleukin-4 and interleukin-13 signaling. Its effectiveness in reducing oral glucocorticoid use in patients with severe asthma while maintaining asthma control is unknown. METHODS: We randomly assigned 210 patients with oral glucocorticoid-treated asthma to receive add-on dupilumab (at a dose of 300 mg) or placebo every 2 weeks for 24 weeks. After a glucocorticoid dose-adjustment period before randomization, glucocorticoid doses were adjusted in a downward trend from week 4 to week 20 and then maintained at a stable dose for 4 weeks. The primary end point was the percentage reduction in the glucocorticoid dose at week 24. Key secondary end points were the proportion of patients at week 24 with a reduction of at least 50% in the glucocorticoid dose and the proportion of patients with a reduction to a glucocorticoid dose of less than 5 mg per day. Severe exacerbation rates and the forced expiratory volume in 1 second (FEV1) before bronchodilator use were also assessed. RESULTS: The percentage change in the glucocorticoid dose was -70.1% in the dupilumab group, as compared with -41.9% in the placebo group (P<0.001); 80% versus 50% of the patients had a dose reduction of at least 50%, 69% versus 33% had a dose reduction to less than 5 mg per day, and 48% versus 25% completely discontinued oral glucocorticoid use. Despite reductions in the glucocorticoid dose, in the overall population, dupilumab treatment resulted in a severe exacerbation rate that was 59% (95% confidence interval [CI], 37 to 74) lower than that in the placebo group and resulted in an FEV1 that was 0.22 liters (95% CI, 0.09 to 0.34) higher. Injection-site reactions were more common with dupilumab than with placebo (9% vs. 4%). Transient blood eosinophilia was observed in more patients in the dupilumab group than in the placebo group (14% vs. 1%). CONCLUSIONS: In patients with glucocorticoid-dependent severe asthma, dupilumab treatment reduced oral glucocorticoid use while decreasing the rate of severe exacerbations and increasing the FEV1. Transient eosinophilia was observed in approximately 1 in 7 dupilumab-treated patients. (Funded by Sanofi and Regeneron Pharmaceuticals; LIBERTY ASTHMA VENTURE ClinicalTrials.gov number, NCT02528214 .).

Zhaoshumycins A and B, Two Unprecedented Antimycin-Type Depsipeptides Produced by the Marine-Derived Streptomyces sp. ITBB-ZKa6.

Marine actinomycetes are prolific chemical sources of complex and novel natural products, providing an excellent chance for new drug discovery. The chemical investigation of the marine-derived Streptomyces sp. ITBB-ZKa6, from Zhaoshu island, Hainan, led to the discovery of two unique antimycin-type depsipeptides, zhaoshumycins A (1) and B (2), along with the isolation of the four known neoantimycins A (3), F (4), D (5), and E (6). The structures of the new compounds 1 and 2 were elucidated on the basis of the analysis of diverse spectroscopic data and biogenetic consideration. Zhaoshumycins A (1) and B (2) represent a new class of depsipeptides, featuring two neoantimycin monomers (only neoantimycin D or neoantimycins D and E) linked to a 1,4-disubstituted benzene ring via an imino group. Initial toxicity tests of 1-6 in MCF7 human breast cancer cells revealed that compounds 5 and 6 possess weak cytotoxic activity. Further structure-activity relationship analysis suggested the importance of the NH2 group at C-34 in 5 and 6 for cytotoxicity in MCF7 cells.

Nonpeptidal compounds from the insect Polyphaga plancyi and their biological evaluation.

Five new nitrogen-containing compounds (1-3, 5, and 6), two compounds which was firstly isolated from natural origin (7 and 10), along with six known ones, were isolated from the ethanol extract of the whole bodies of Polyphaga plancyi. The structures of the new compounds including their absolute configurations at stereogenic centers were assigned on the basis of spectroscopic analyses and computational methods. Racemic 10 was separated by chiral HPLC. Biological activities of these isolates against extracellular matrix components in rat renal proximal tubular cells, EV71, COX-2, ROCK2, JAK3, and tuberculosis were evaluated. Importantly, 8 was found to be a selective Smad3 phosphorylation inhibitor.

Sulfur and nitrogen-containing compounds from the whole bodies of Blaps japanensis.

Pipajiains H-J (1-3), three new phenolic derivatives with an unusual sulfone group, pipajiamides A-C (4-6), three new amide derivatives, pipajiaine A (7), one new imidazole analogue, and pipajiaine B (8), a pair of new pyrrolidine derivatives, along with three known compounds were isolated from the insect Blaps japanensis. Their structures were identified by spectroscopic and computational methods. Chiral HPLC was used to separate the (-)- and (+)-antipodes of 4 and 8. Biological activities of all the new compounds against extracellular matrix in rat renal proximal tubular cells, human cancer cells (A549, Huh-7, and K562), COX-2, ROCK1, and JAK3 were evaluated. The results show that compounds 2, (+)-4, and (-)-4 are active against kidney fibrosis, whereas, compound 9 is active toward human cancer cells, inflammation, and JAK3 kinase.

[Genetic analysis of a patient with late infantile metachromatic leukodystrophy].

OBJECTIVE: To detect variants of ARSA gene in a child featuring late infantile metachromatic leukodystrophy (MLD). METHODS: PCR and Sanger sequencing was carried out for the patient and her parents. RESULTS: The patient had typical features of MLD including ARSA deficiency, regression of walking ability, and demyelination. Compound heterozygous variants of the ARSA gene, namely c.960G>A and c.244C>T, were detected in the patient, for which her mother and father were respectively heterozygous carriers. ARSA c.960G>A was known to be pathogenic, while ARSA c.244C>T was a novel variant. The same variants were not detected among 50 healthy controls. CONCLUSION: The compound heterozygous variants c.960G>A and c.244C>T of the ARSA gene probably underlie the MLD in this patient.

N-containing compounds from Periplaneta americana and their activities against wound healing.

Three new compounds, periplanamides A (1) and B (2), periplanpyrazine A (3), a new naturally occurring compound salicyluric acid methyl ester (6), and seventeen known compounds were isolated from the medicinal insect Periplaneta americana. The structures of the new compounds were elucidated on the basis of spectroscopic methods. The absolute configurations of 2 were assigned by computational methods. Biological activities of these isolates except 1, 9, 11, and 13 toward nitric oxide (NO) production, cell proliferation in HDFs, cell migration and angiogenesis in HUVECs were evaluated.

[A novel compound heterozygous mutation of GNPTAB gene underlying a case with mucolipidosis type II α/ß].

OBJECTIVE: To analyze the clinical features and genetic mutations in a patient with mucolipidosis type II α/ß by using next generation sequencing. METHODS: Clinical data of the patient was collected. Genomic DNA of the patient and her parents was extracted by a standard method. The patient was subjected to targeted sequencing using an Ion Ampliseq panel, which included genes related to mucolipidosis and mucopolysaccharidosis. Suspected mutations were verified by Sanger sequencing. RESULTS: Compound heterozygous mutations, namely c.1284+1G>T and c.1090C>T (p.Arg364*), were detected in the patient, which were respectively inherited from her mother and father. No other disease-causing mutation was detected in the patient. GNPTAB c.1090C>T was known to be pathogenic, while GNPTAB c.1284+1G>T is a novel mutation. The same mutations were not detected among 50 healthy controls. CONCLUSION: The compound heterozygous mutations c.1284+1G>T and c.1090C>T (p.Arg364*) of GNPTAB gene probably account for the mucolipidosis type II α/ß in the patient. NGS has a great value for the molecular diagnosis and typing of mucolipidosis.

Comparing the evolutionary conservation between human essential genes, human orthologs of mouse essential genes and human housekeeping genes.

Human housekeeping genes are often confused with essential human genes, and several studies regard both types of genes as having the same level of evolutionary conservation. However, this is not necessarily the case. To clarify this, we compared the differences between human housekeeping genes and essential human genes with respect to four aspects: the evolutionary rate (dN/dS), protein sequence identity, single-nucleotide polymorphism (SNP) density and level of linkage disequilibrium (LD). The results showed that housekeeping genes had lower evolutionary rates, higher sequence identities, lower SNP densities and higher levels of LD compared with essential genes. Together, these findings indicate that housekeeping and essential genes are two distinct types of genes, and that housekeeping genes have a higher level of evolutionary conservation. Therefore, we suggest that researchers should pay careful attention to the distinctions between housekeeping genes and essential genes. Moreover, it is still controversial whether we should substitute human orthologs of mouse essential genes for human essential genes. Therefore, we compared the evolutionary features between human orthologs of mouse essential genes and human housekeeping genes and we got inconsistent results in long-term and short-term evolutionary characteristics implying the irrationality of simply replacing human essential genes with human orthologs of mouse essential genes.

Metabolic network failures in Alzheimer's disease: A biochemical road map.

INTRODUCTION: The Alzheimer's Disease Research Summits of 2012 and 2015 incorporated experts from academia, industry, and nonprofit organizations to develop new research directions to transform our understanding of Alzheimer's disease (AD) and propel the development of critically needed therapies. In response to their recommendations, big data at multiple levels are being generated and integrated to study network failures in disease. We used metabolomics as a global biochemical approach to identify peripheral metabolic changes in AD patients and correlate them to cerebrospinal fluid pathology markers, imaging features, and cognitive performance. METHODS: Fasting serum samples from the Alzheimer's Disease Neuroimaging Initiative (199 control, 356 mild cognitive impairment, and 175 AD participants) were analyzed using the AbsoluteIDQ-p180 kit. Performance was validated in blinded replicates, and values were medication adjusted. RESULTS: Multivariable-adjusted analyses showed that sphingomyelins and ether-containing phosphatidylcholines were altered in preclinical biomarker-defined AD stages, whereas acylcarnitines and several amines, including the branched-chain amino acid valine and α-aminoadipic acid, changed in symptomatic stages. Several of the analytes showed consistent associations in the Rotterdam, Erasmus Rucphen Family, and Indiana Memory and Aging Studies. Partial correlation networks constructed for Aß1-42, tau, imaging, and cognitive changes provided initial biochemical insights for disease-related processes. Coexpression networks interconnected key metabolic effectors of disease. DISCUSSION: Metabolomics identified key disease-related metabolic changes and disease-progression-related changes. Defining metabolic changes during AD disease trajectory and its relationship to clinical phenotypes provides a powerful roadmap for drug and biomarker discovery.

Chemical structure informing statistical hypothesis testing in metabolomics.

MOTIVATION: Metabolomics has been shown as an effective tool to study various biological and biomedical phenotypes, whereas interrogating the inherently noisy metabolite concentration data with limited sample size remains a major challenge. Accumulating evidence suggests that metabolites' structures are relevant to their bioactivities. RESULTS: We present a new strategy to boost the statistical power of hypothesis testing in metabolomics by incorporating quantitative molecular descriptors for each metabolite. The strategy selects potentially informative summary molecular descriptors and outputs chemical structure-informed false discovery rates. The effectiveness of the proposed strategy is demonstrated by both simulation studies and a real application. In a metabolomic study on Alzheimer's disease, the posterior inclusion probability for summary molecular descriptors reaches 0.97. By incorporating the structure data, our approach uniquely identifies multiple Alzheimer's disease signatures, which are consistent with existing evidence. These results evidently suggest the value of the proposed approach for metabolomic hypothesis-testing problems. AVAILABILITY AND IMPLEMENTATION: A code package implementing the strategy is freely available at https://github.com/HongjieZhu/CIMA.git.