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Background The mutations changing the expression level of a gene, or expression quantitative trait loci (eQTL), can be identified by testing the association between genetic variants and gene expression in multiple individuals (eQTL mapping), or by comparing the expression of the alleles in a heterozygous individual (allele specific expression or ASE analysis). The aims of the study were to find and compare ASE and local eQTL in 4 bovine RNA-sequencing (RNA-Seq) datasets, validate them in an independent ASE study and investigate if they are associated with complex trait variation. Results We present a novel method for distinguishing between ASE driven by polymorphisms in cis and parent of origin effects. We found that single nucleotide polymorphisms (SNPs) driving ASE are also often local eQTL and therefore presumably cis eQTL. These SNPs often, but not always, affect gene expression in multiple tissues and, when they do, the allele increasing expression is usually the same. However, there were systematic differences between ASE and local eQTL and between tissues and breeds. We also found that SNPs significantly associated with gene expression (p

Background A comprehensive understanding of DNA adducts, one of the most plausible origins of cancer mutations, is still elusive, especially in human tissues in clinical settings. Recent technological developments have facilitated the identification of multiple DNA adducts in a single experiment. Only a few attempts toward this “DNA adductome approach” in human tissues have been reported. Geospatial information on DNA adducts in human organs has been scarce. Aim Mass spectrometry of human gastric mucosal DNA was performed to identify DNA adducts associated with environmental factors. Materials and methods From 59 subjects who had received gastrectomy for gastric cancer, 306 samples of nontumor tissues and 15 samples of tumors (14 cases) were taken for DNA adductome analysis. Gastric nontumor tissue from autopsies of 7 subjects without gastric cancer (urothelial cancer, hepatocellular carcinoma, lung cancer each; the other four cases were without any cancers) was also investigated. Briefly, DNA was extracted from each sample with antioxidants, digested into nucleosides, separated by liquid chromatography, and then electrospray-ionized. Specific DNA adducts were identified by mass/charge number and column retention time compared to standards. Information on lifestyle factors such as tobacco smoking and alcohol drinking was taken from the clinical records of each subject. Results Seven DNA adducts, including modified bases, C5-methyl-2′-deoxycytidine, 2′-deoxyinosine, C5-hydroxymethyl-2′-deoxycytidine, N6-methyl-2′-deoxyadenosine, 1,N6-etheno-2′-deoxyadenosine, N6-hydroxymethyl-2′-deoxyadenosine, and C8-oxo-2′-deoxyguanosine, were identified in the human stomach and characterized. Intraindividual differences according to the multiple sites of these adducts were noted but were less substantial than interindividual differences. N6-hydroxymethyl-2′-deoxyadenosine was identified in the human stomach for the first time. The amount of C5-hydroxymethyl-2′-deoxycytidine was higher in the stomachs of subjects without gastric cancer than in the nontumor and tumor portions of the stomach in gastric cancer patients. Higher levels of 1,N6-etheno-2′-deoxyadenosine were detected in the subjects who reported both smoking and drinking than in those without these habits. These DNA adducts showed considerable correlations with each other. Conclusions We characterized 7 DNA adducts in the nontumor portion of the human stomach in both gastric cancer subjects and nongastric cancer subjects. A reduction in C5-hydroxymethyl-dC even in the nontumor mucosa of patients with gastric cancer was observed. Smoking and drinking habits significantly influenced the quantity of one of the lipid peroxidation-derived adducts, etheno-dA. A more expansive DNA adductome profile would provide a comprehensive understanding of the origin of human cancer in the future.

Background Plant transitions to land require robust cell walls for regulatory adaptations and to resist changing environments. Cell walls provide essential plasticity for plant cell division and defense, which are often conferred by the expansin superfamily with cell wall-loosening functions. However, the evolutionary mechanisms of expansin during plant terrestrialization are unclear. Results Here, we identified 323 expansin proteins in 12 genomes from algae to angiosperms. Phylogenetic evolutionary, structural, motif gain and loss and Ka/Ks analyses indicated that highly conserved expansin proteins were already present in algae and expanded and purified after plant terrestrialization. We found that the expansion of the FtEXPA subfamily was caused by duplication events and that the functions of certain duplicated genes may have differentiated. More importantly, we generated space-time expression profiles and finally identified five differentially expressed FtEXPs in both large and small fruit Tartary buckwheat that may regulate fruit size by responding to indoleacetic acid. Conclusions A total of 323 expansin proteins from 12 representative plants were identified in our study during terrestrialization, and the expansin family that originated from algae expanded rapidly after the plants landed. The EXPA subfamily has more members and conservative evolution in angiosperms. FtEXPA1, FtEXPA11, FtEXPA12, FtEXPA19 and FtEXPA24 can respond to indole-3-acetic acid (IAA) signals and regulate fruit development. Our study provides a blueprint for improving the agronomic traits of Tartary buckwheat and a reference for defining the evolutionary history of the expansin family during plant transitions to land.

Background Lysine succinylation is a naturally occurring post-translational modification (PTM) that is ubiquitous in organisms. Lysine succinylation plays important roles in regulating protein structure and function as well as cellular metabolism. Global lysine succinylation at the proteomic level has been identified in a variety of species; however, limited information on lysine succinylation in plant species, especially paper mulberry, is available. Paper mulberry is not only an important plant in traditional Chinese medicine, but it is also a tree species with significant economic value. Paper mulberry is found in the temperate and tropical zones of China. The present study analyzed the effects of lysine succinylation on the growth, development, and physiology of paper mulberry. Results A total of 2097 lysine succinylation sites were identified in 935 proteins associated with the citric acid cycle (TCA cycle), glyoxylic acid and dicarboxylic acid metabolism, ribosomes and oxidative phosphorylation; these pathways play a role in carbon fixation in photosynthetic organisms and may be regulated by lysine succinylation. The modified proteins were distributed in multiple subcellular compartments and were involved in a wide variety of biological processes, such as photosynthesis and the Calvin-Benson cycle. Conclusion Lysine-succinylated proteins may play key regulatory roles in metabolism, primarily in photosynthesis and oxidative phosphorylation, as well as in many other cellular processes. In addition to the large number of succinylated proteins associated with photosynthesis and oxidative phosphorylation, some proteins associated with the TCA cycle are succinylated. Our study can serve as a reference for further proteomics studies of the downstream effects of succinylation on the physiology and biochemistry of paper mulberry.

Background A body distribution with high intramuscular fat and low abdominal fat is the ideal goal for broiler breeding. Preadipocytes with different origins have differences in terms of metabolism and gene expression. The transcriptome analysis performed in this study of intramuscular preadipocytes (DIMFPs) and adipose tissue-derived preadipocytes (DAFPs) aimed to explore the characteristics of lipid deposition in different chicken preadipocytes by dedifferentiation in vitro. Results Compared with DAFPs, the total lipid content in DIMFPs was reduced (P ). Moreover, 72 DEGs related to lipid metabolism were screened, which were involved in adipocyte differentiation, fatty acid transport and fatty acid synthesis, lipid stabilization, and lipolysis. Among the 72 DEGs, 19 DEGs were enriched in the PPAR signaling pathway, indicating its main contribution to the regulation of the difference in lipid deposition between DAFPs and DIMFPs. Among these 19 genes, the representative APOA1, ADIPOQ, FABP3, FABP4, FABP7, HMGCS2, LPL and RXRG genes were downregulated, but the ACSL1, FABP5, PCK2, PDPK1, PPARG, SCD, SCD5, and SLC27A6 genes were upregulated (P P Conclusions Our data suggested a difference in lipid deposition between DIMFPs and DAFPs of chickens in vitro and proposed a molecular regulatory network for the difference in lipid deposition between chicken DAFPs and DIMFPs. The lipid content was significantly increased in DAFPs by the direct mediation of PPAR signaling pathways. These findings provide new insights into the regulation of tissue-specific fat deposition and the optimization of body fat distribution in broilers.

Background The presence of small supernumerary marker chromosomes (sSMCs) in a karyotype leads to diagnostic questions because the resulting extra material may cause abnormal development depending on the origin of the duplication/triplication. Because SMCs are so small, their origin cannot be determined by conventional cytogenetic techniques, and new molecular cytogenetic methods are necessary. Here, we applied a target approach to chromosome rearrangement analysis by isolating a chromosome of interest via microdissection and using it in fluorescence in situ hybridization (FISH) as a probe in combination with whole-chromosome painting probes. This approach allows to identify origins of both the euchromatin and repeat-rich regions of a marker. Case presentation We report a case of an adult male with congenital atresia of the rectum and anus, anotia, and atresia of the external auditory canal along with hearing loss. Karyotyping and FISH analysis with whole-chromosome painting probes of acrocentric chromosomes and the constructed microdissection library of the marker chromosome reliably identified an additional chromosome in some metaphases: mos 47,XY,+idic(22)(q11.2)[14]/46,XY [23]. Conclusion We propose to use whole-chromosome libraries and microdissected chromosomes in FISH to identify SMCs enriched with repeated sequences. We show that the methodology is successful in identifying the composition of a satellited marker chromosome.

Dermanura Gervais, 1856 is represented by small frugivorous bats of the Stenodermatinae subfamily. The taxonomy of this group presents controversies and has been subject to changes, especially since the morphological characters evaluated have left gaps that are difficult to fill regarding good species characterization. Previous studies performed in Dermanura cinerea Gervais, 1856 found that the karyotype of this species has a diploid number of chromosomes equal to 30 and 56 autosomal arms. The objective of the present study was to describe, for the first time, the karyotypes of the species Dermanura anderseni (Osgood, 1916) and Dermanura gnoma (Handley, 1987) based on classical cytogenetic markers. For both species, the diploid number found was 2n = 30 and NFa = 56. Two pairs of chromosomes showed markings of the nucleolus organizing regions (AgNORs) in the species D. anderseni and only one pair in D. gnoma, differing from what has already been described for D. cinerea. The two species analyzed here also showed differences in the sex chromosome system, with D. gnoma showing a neo-XY type system while in D. anderseni the classic XY sexual system was observed. In both species, visualization of the constitutive heterochromatin occurred in the pericentromeric region of all chromosomes, as well as in the short arms of the subtelocentric chromosomes. The present work represents an important expansion of karyotypic information for the subfamily Stenodermatinae, bringing chromosomal features that are possible to use in the taxonomic implications of the group.

Background The OncoScan microarray assay (OMA) using highly multiplexed molecular inversion probes for single nucleotide polymorphism (SNP) loci enabled the detection of cytogenomic abnormalities of chromosomal imbalances and pathogenic copy number variants (pCNV). The small size of molecular inversion probes is optimal for SNP genotyping of fragmented DNA from fixed tissues. This retrospective study evaluated the clinical utility of OMA as a uniform platform to detect cytogenomic abnormalities for pregnancy loss from fresh and fixed tissues of products of conception (POC). Results Fresh specimens of POC were routinely subjected to cell culture and then analyzed by karyotyping. POC specimens with a normal karyotype (NK) or culture failure (CF) and from formalin-fixed paraffin-embedded (FFPE) tissues were subjected to DNA extraction for OMA. The abnormality detection rate (ADR) by OMA on 94 cases of POC-NK, 38 cases of POC-CF, and 35 cases of POC-FFPE tissues were 2% (2/94), 26% (10/38), and 57% (20/35), respectively. The detected cytogenomic abnormalities of aneuploidies, triploidies and pCNV accounted for 50%, 40% and 10% in POC-CF and 85%, 10% and 5% in POC-FFPE, respectively. False negative result from cultured maternal cells and maternal cell contamination were each detected in one case. OMA on two cases with unbalanced structural chromosome abnormalities further defined genomic imbalances and breakpoints. Conclusion OMA on POC-CF and POC-FFPE showed a high diagnostic yield of cytogenomic abnormalities. This approach circumvented the obstacles of CF from fresh specimens and fragmented DNA from fixed tissues and provided a reliable and effective platform for detecting cytogenomic abnormalities and monitoring true fetal result from maternal cell contamination.

Allisandra K Rha,1 Anne S Maguire,1,2 Douglas R Martin1,2 1Scott-Ritchey Research Center, Auburn University, Auburn, AL, 36849, USA; 2Department of Anatomy, Physiology, and Pharmacology, Auburn University College of Veterinary Medicine, Auburn, AL, 36849, USACorrespondence: Douglas R MartinScott-Ritchey Research Center, Auburn University, 1265 H.C. Morgan Drive, Auburn, AL, 36849, USATel +1 334 844 5951Email martidr@auburn.eduAbstract: The lysosomal storage disorder, GM1 gangliosidosis (GM1), is a neurodegenerative condition resulting from deficiency of the enzyme β-galactosidase (β-gal). Mutation of the GLB1 gene, which codes for β-gal, prevents cleavage of the terminal β-1,4-linked galactose residue from GM1 ganglioside. Subsequent accumulation of GM1 ganglioside and other substrates in the lysosome impairs cell physiology and precipitates dysfunction of the nervous system. Beyond palliative and supportive care, no FDA-approved treatments exist for GM1 patients. Researchers are critically evaluating the efficacy of substrate reduction therapy, pharmacological chaperones, enzyme replacement therapy, stem cell transplantation, and gene therapy for GM1. A Phase I/II clinical trial for GM1 children is ongoing to evaluate the safety and efficacy of adeno-associated virus-mediated GLB1 delivery by intravenous injection, providing patients and families with hope for the future.Keywords: GM1 gangliosidosis, gene therapy, biomarkers, chaperone, GLB1, LSD

Background With the development of third-generation sequencing (TGS) technologies, people are able to obtain DNA sequences with lengths from 10s to 100s of kb. These long reads allow protein domain annotation without assembly, thus can produce important insights into the biological functions of the underlying data. However, the high error rate in TGS data raises a new challenge to established domain analysis pipelines. The state-of-the-art methods are not optimized for noisy reads and have shown unsatisfactory accuracy of domain classification in TGS data. New computational methods are still needed to improve the performance of domain prediction in long noisy reads. Results In this work, we introduce ProDOMA, a deep learning model that conducts domain classification for TGS reads. It uses deep neural networks with 3-frame translation encoding to learn conserved features from partially correct translations. In addition, we formulate our problem as an open-set problem and thus our model can reject reads not containing the targeted domains. In the experiments on simulated long reads of protein coding sequences and real TGS reads from the human genome, our model outperforms HMMER and DeepFam on protein domain classification. Conclusions In summary, ProDOMA is a useful end-to-end protein domain analysis tool for long noisy reads without relying on error correction.

Background Trichophyton mentagrophyte (TM), a zoonotic pathogen, has been endangering public health due to emerging drug resistance. Although increased attention is paid to this issue, there is very limited research available on drug resistance in TM. In this study, we studied the gene and proteomic changes, morphological changes, cellular fat localization, fat content changes, and biofilm of TM treated with different substances. Results The TM growth curve showed a positive correlation with the concentration of Fenarimol (FE), genistein (GE), clotrimazole (KM), and Miconazole nitrate salt (MK). The morphology of TM cells changed in different degrees after treatment with different substances as observed by TEM and SEM. The results showed that under KM and berberine hydrochloride (BB) treatment, a total of 3305 differentially expressed genes were detected, with the highest number in the KM-treated group (578 up-regulated and 615 down-regulated). A total of 847 proteins and 1850 peptides were identified in TM proteomics. Nile red staining showed that the fat content of TM was significantly higher in the BB-, ethidium bromide- (EB), FE-, KM-, Adriamycin hydrochloride- (YA), and MK-treated group compared to the control group. Results of the biofilm thickness showed that it gradually increased under treatment with specific concentrations of KM or BB, which may be related to the up-regulation of ERG25 and CYP related gene proteins. Conclusions It is suggested that in order to effectively deal with dermatomycosis caused by TM, it is necessary to inhibit the expression of ERG25 and CYP related genes and fat metabolism, which can result in the inhibition of the production of biofilm by the fungus and solve the problem of fungal drug resistance in clinical settings.

Background Transposable elements are significant components of most organism’s genomes, yet the reasons why their abundances vary significantly among species is poorly understood. A recent study has suggested that even in the absence of traditional molecular evolutionary explanations, transposon proliferation may occur through a process known as ‘transposon engineering’. However, their model used a fixed beneficial transposon insertion frequency of 20%, which we believe to be unrealistically high. Results Reducing this beneficial insertion frequency, while keeping all other parameters identical, prevented transposon proliferation. Conclusions We conclude that the author’s original findings are better explained through the action of positive selection rather than ‘transposon engineering’, with beneficial insertion effects remaining important during transposon proliferation events.

Motivation: De Bruijn graphs play an essential role in computational biology, facilitating rapid alignment-free comparison of genomic datasets as well as reconstruction of underlying genomic sequences. Subsequently, an important question is how to efficiently represent, compress, and transmit de Bruijn graphs of the most common types of genomic data sets, such as sequencing reads, genomes, and pan-genomes. Results: We introduce simplitigs, an effective representation of de Bruijn graphs for alignment-free applications. Simplitigs are a generalization of unitigs and correspond to spellings of vertex-disjoint paths in a de Bruijn graph. We present an easy-to-plug-in greedy heuristic for their computation and provide a reference implementation in a program called ProphAsm. We use ProphAsm to compare the scaling of simplitigs and unitigs on a range of genomic datasets. We demonstrate that simplitigs are superior to unitigs in terms of the cumulative sequence length as well as of the number of sequences, and that they are sufficiently close to the theoretical bounds for practical applications. Finally, we demonstrate that, when combined with standard full-text indexes, simplitigs provide a scalable solution for k-mer search in pan-genomes. Availability: ProphAsm is written in C++ and is available under the MIT license from http://github.com/prophyle/prophasm.

Yosra Zaimi,1 Myriam Ayari,1 Asma Mensi,1 Linda Bel Hadj Kacem,2 Leila Achouri,3 Meriem Bouzrara,4 Yosra Said,1 Leila Mouelhi,1 Radhouane Debbeche1 1Department of Gastroenterology, Charles Nicolle Hospital, Tunis, Tunisia; 2Department of Pathology, Charles Nicolle Hospital, Tunis, Tunisia; 3Department of Oncologic Surgery, University of Tunis El Manar, Tunis, Tunisia; 4Department of Radiology, Charles Nicolle Hospital, Tunis, TunisiaCorrespondence: Myriam AyariDepartment of Gastroenterology, Charles Nicolle Hospital, Boulevard 9 Avril 1938 Bab Saâdoun, Tunis, 1006, TunisiaEmail ayari.myriam@hotmail.frAbstract: H syndrome is an extremely rare autosomal recessive affection caused by biallelic mutations in the SLC29A3 gene encoding the human equilibrative nucleoside transporter hENT3. The hallmark signs are cutaneous consisting of hyperpigmentation and hypertrichosis patches. Besides, associated systemic manifestations are highly various reflecting phenotypic pleiotropism. Herein, we report a first case of pseudo-Meigs’ syndrome occurring in a young Tunisian H syndrome diagnosed patient with a novel homozygous frameshift mutation in exon 2 of the SLC29A3 gene: p.S15Pfs*86 inducing a premature stop codon. The patient developed ascites associated with left ovarian mass and she underwent surgery. After tumor resection, ascites disappeared rapidly. Histological examination showed serous cystadenoma of the ovary orienting the diagnosis towards pseudo-Meigs’ syndrome.Keywords: H syndrome, SLC29A3 gene, rare disease, pseudo-Meigs’ syndrome, Tunisian patient

Background Antibiotic-producing Streptomyces bacteria are ubiquitous in nature, yet most studies of its diversity have focused on free-living strains inhabiting diverse soil environments and those in symbiotic relationship with invertebrates. Results We studied the draft genomes of 73 Streptomyces isolates sampled from the skin (wing and tail membranes) and fur surfaces of bats collected in Arizona and New Mexico. We uncovered large genomic variation and biosynthetic potential, even among closely related strains. The isolates, which were initially identified as three distinct species based on sequence variation in the 16S rRNA locus, could be distinguished as 41 different species based on genome-wide average nucleotide identity. Of the 32 biosynthetic gene cluster (BGC) classes detected, non-ribosomal peptide synthetases, siderophores, and terpenes were present in all genomes. On average, Streptomyces genomes carried 14 distinct classes of BGCs (range = 9–20). Results also revealed large inter- and intra-species variation in gene content (single nucleotide polymorphisms, accessory genes and singletons) and BGCs, further contributing to the overall genetic diversity present in bat-associated Streptomyces. Finally, we show that genome-wide recombination has partly contributed to the large genomic variation among strains of the same species. Conclusions Our study provides an initial genomic assessment of bat-associated Streptomyces that will be critical to prioritizing those strains with the greatest ability to produce novel antibiotics. It also highlights the need to recognize within-species variation as an important factor in genetic manipulation studies, diversity estimates and drug discovery efforts in Streptomyces.

BackgroundVernalization is a type of low temperature stress used to promote rapid bolting and flowering in plants. Although rapid bolting and flowering promote the reproduction of Chinese cabbages (Brassica rapaL.ssp. pekinensis), this process causes their commercial value to decline. Clarifying the mechanisms of vernalization is essential for its further application. We performed RNA sequencing of gradient-vernalization in order to explore the reasons for the different bolting process of two Chinese cabbage accessions during vernalization.ResultsThere was considerable variation in gene expression between different-bolting Chinese cabbage accessions during vernalization. Comparative transcriptome analysis and weighted gene co-expression network analysis (WGCNA) were performed for different-bolting Chinese cabbage during different vernalization periods. The biological function analysis and hub gene annotation of highly relevant modules revealed that shoot system morphogenesis and polysaccharide and sugar metabolism caused early-bolting ‘XBJ’ to bolt and flower faster; chitin, ABA and ethylene-activated signaling pathways were enriched in late-bolting ‘JWW’; and leaf senescence and carbohydrate metabolism enrichment were found in the two Chinese cabbage-related modules, indicating that these pathways may be related to bolting and flowering. The high connectivity of hub genes regulated vernalization, includingMTHFR2,CPRD49,AAP8, endoglucanase 10,BXLs,GATLs, andWRKYs. Additionally, five genes related to flower development,BBX32(binds to theFTpromoter),SUS1(increasesFTexpression),TSF(the closest homologue ofFT),PAOandNAC029(plays a role in leaf senescence), were expressed in the two Chinese cabbage accessions.ConclusionThe present work provides a comprehensive overview of vernalization-related gene networks in two different-bolting Chinese cabbages during vernalization. In addition, the candidate pathways and hub genes related to vernalization identified here will serve as a reference for breeders in the regulation of Chinese cabbage production.

Background It has been postulated that the interaction between environmental risk factors and genetic susceptibility is a possible cause for the development of acute myeloid leukemia (AML). Cytochrome P450 (CYP) detoxification enzymes are responsible for the elimination of oxidative stress. Genetic polymorphisms in these enzymes may cause AML due to enhanced accumulation of reactive oxygen species. To study the association between CYP3A4 (A290G) and CYP2B6 (G516T) gene polymorphisms and the predisposition and prognosis of AML, 50 upfront AML patients and 50 healthy individuals were genotyped for CYP2B6 (G516T) and CYP3A4 (A290G) single-nucleotide polymorphisms (SNPs) using polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP) technique. The polymorphisms were evaluated in relation to the response to chemotherapy and survival. Results CYP2B6 gene mutation carries a threefold risk of developing AML (odds ratio [OR], 3.0; 95% confidence interval [CI], 1.3–6.9), whereas CYP3A4 gene mutation carries approximately fourfold risk (OR, 3.8; 95% CI, 1.4–10.1). The presence of combined gene mutation conferred about 15-fold increased risk of developing AML compared with the presence of a single gene mutation (OR, 14.8; 95% CI, 1.8–124.2). CYP3A4 gene mutation is associated with worse overall survival (P = 0.030). Conclusion CYP enzyme gene polymorphisms are associated with the development of AML. Elimination of oxidative stress in genetically susceptible individuals may decrease the risk of AML and may improve survival.

Background Jasmonates (JAs) are important for plants to coordinate growth, reproduction, and defense responses. In JA signaling, jasmonate ZIM-domain (JAZ) proteins serve as master regulators at the initial stage of herbivores attacks. Although discovered in many plant species, little in-depth characterization of JAZ gene expression has been reported in the agronomically important crop, maize (Zea mays L.). Results In this study 16 JAZ genes from the maize genome were identified and classified. Phylogenetic analyses were performed from maize, rice, sorghum, Brachypodium, and Arabidopsis using deduced protein sequences, total six clades were proposed and conservation was observed in each group, such as similar gene exon/intron structures. Synteny analysis across four monocots indicated these JAZ gene families had a common ancestor, and duplication events in maize genome may drive the expansion of JAZ gene family, including genome-wide duplication (GWD), transposon, and/or tandem duplication. Strong purifying selection acted on all JAZ genes except those in group 4, which were under neutral selection. Further, we cloned three paralogous JAZ gene pairs from two maize inbreds differing in JA levels and insect resistance, and gene polymorphisms were observed between two inbreds. Conclusions Here we analyzed the composition and evolution of JAZ genes in maize with three other monocot plants. Extensive phylogenetic and synteny analysis revealed the expansion and selection fate of maize JAZ. This is the first study comparing the difference between two inbreds, and we propose genotype-specific JAZ gene expression might be present in maize plants. Since genetic redundancy in JAZ gene family hampers our understanding of their role in response to specific elicitors, we hope this research could be pertinent to elucidating the defensive responses in plants.

Background Diagnosis of breast cancer is more complicated due to lack of minimal invasive biomarker with sufficient precision. DNA methylation is a promising marker for cancer diagnosis. In this study, authors evaluated methylation patterns for PTEN and SMAD4 in blood samples using EpiTect Methyl II QPCR assay quantitative PCR technology. Results Methylation status for PTEN and SMAD4 were statistically significant as breast cancer patients reported hypermethylation compared to benign and control groups (77.1 ± 17.9 vs. 24.9 ± 4.5 and 15.1 ± 1.4 and 70.1 ± 14.4 vs. 28.2 ± 0.61 and 29.5 ± 3.6, respectively). ROC curve analysis revealed that both PTEN (AUC = 0.992) and SMAD4 (AUC = 0.853) had good discriminative power for differentiating BC from all non-cancer individuals (benign and healthy combined) compared to routine tumor markers CEA (AUC = 0.538) and CA15.3 (AUC = 0.686). High PTEN methylation degree was associated with late stages (84.2 ± 17.4), positive lymph node (84.2 ± 18.5), positive ER (81.3 ± 19.7), positive PgR (79.5 ± 19.1), and positive HER2 (80.7 ± 19.0) vs. 67.4 ± 13.8, 70.6 ± 14.8, 72.8 ± 14.9, 72.5 ± 14.7, and 70.2 ± 13.5 in early stages, negative lymph node, negative ER, negative PgR, and negative HER2, respectively. Similar results were obtained regarding SMAD4 methylation. Sensitivity, specificity, positive and negative predictive values, and accuracy for methylated PTEN were 100%, 95%, 99.1%, 100%, and 95%, respectively when differentiated BC from all-non cancer controls. Interestingly, PTEN could distinguish early BC stages with good sensitivity 84.4%, 51.4%, 69.1%, 72%, and 70%, respectively. Conclusion Methylation status of PTEN and SMAD4 is a promising blood marker for early detection of breast cancer. Future studies are needed for their role as prognostic markers.

Background Commelinaceae (Commelinales) comprise 41 genera and are widely distributed in both the Old and New Worlds, except in Europe. The relationships among genera in this family have been suggested in several morphological and molecular studies. However, it is difficult to explain their relationships due to high morphological variations and low support values. Currently, many researchers have been using complete chloroplast genome data for inferring the evolution of land plants. In this study, we completed 15 new plastid genome sequences of subfamily Commelinoideae using the Mi-seq platform. We utilized genome data to reveal the structural variations and reconstruct the problematic positions of genera for the first time. Results All examined species of Commelinoideae have three pseudogenes (accD, rpoA, and ycf15), and the former two might be a synapomorphy within Commelinales. Only four species in tribe Commelineae presented IR expansion, which affected duplication of the rpl22 gene. We identified inversions that range from approximately 3 to 15 kb in four taxa (Amischotolype, Belosynapsis, Murdannia, and Streptolirion). The phylogenetic analysis using 77 chloroplast protein-coding genes with maximum parsimony, maximum likelihood, and Bayesian inference suggests that Palisota is most closely related to tribe Commelineae, supported by high support values. This result differs significantly from the current classification of Commelinaceae. Also, we resolved the unclear position of Streptoliriinae and the monophyly of Dichorisandrinae. Among the ten CDS (ndhH, rpoC2, ndhA, rps3, ndhG, ndhD, ccsA, ndhF, matK, and ycf1), which have high nucleotide diversity values (Pi > 0.045) and over 500 bp length, four CDS (ndhH, rpoC2, matK, and ycf1) show that they are congruent with the topology derived from 77 chloroplast protein-coding genes. Conclusions In this study, we provide detailed information on the 15 complete plastid genomes of Commelinoideae taxa. We identified characteristic pseudogenes and nucleotide diversity, which can be used to infer the family evolutionary history. Also, further research is needed to revise the position of Palisota in the current classification of Commelinaceae.

MeliponaIlliger, 1806 is represented by 74 known species of stingless bees, distributed throughout the Neotropical region. Cytogenetically it is the most studied stingless bee genus of the tribe Meliponini. Member species are divided in two groups based on the volume of heterochromatin. This study aim was to analyze the composition and organization of chromatin of the stingless bee subspeciesMelipona seminigra merrillaeCockerell, 1919 using classical and molecular cytogenetic techniques, so contributing to a better understanding of the processes of chromosomal changes within the genus. We confirm thatM. seminigra merrillaehas a chromosome number of 2n = 22 and n = 11, results that differ from those reported for the genus in the absence of B chromosomes. The heterochromatic pattern revealed a karyotype composed of chromosomes with a high heterochromatin content, which makes it difficult to visualize the centromere. Silver nitrate impregnation (Ag-NOR) showed transcriptionally active sites on the second chromosomal pair. Staining of base-specific fluorophores DAPI-CMA3indicated a homogeneous distribution of intensely DAPI-stained heterochromatin, while CMA3markings appeared on those terminal portions of the chromosomes corresponding to euchromatin. Similar to Ag-NOR, fluorescence in situ hybridization (FISH) with 18S ribosomal DNA probe revealed distinct signals on the second pair of chromosomes. Microsatellite mapping (GA)15showed markings distributed in euchromatic regions, while mapping with (CA)15showed marking patterns in heterochromatic regions, together with a fully marked chromosome pair. Microsatellite hybridization, both in heterochromatic and euchromatic regions, may be related to the activity of transposable elements. These are capable of forming new microsatellites that can be dispersed and amplified in different regions of the genome, demonstrating that repetitive sequences can evolve rapidly, thus resulting in within-genus diversification.

A clinical trial using adeno-associated virus serotype 8 (AAV8)-human uridine diphosphate glucuronosyltransferase 1A1 (hUGT1A1) to treat inherited severe unconjugated hyperbilirubinemia (Crigler-Najjar syndrome) is ongoing, but preclinical data suggest that long-term efficacy in children is impaired due to loss of transgene expression upon hepatocyte proliferation in a growing liver. This study aims to determine at what age long-term efficacy can be obtained in the relevant animal model and whether immune modulation allows re-treatment using the same AAV vector. Neonatal, suckling, and juvenile Ugt1a1-deficient rats received a clinically relevant dose of AAV8-hUGT1A1, and serum bilirubin levels and anti-AAV8 neutralizing antibodies (NAbs) in serum were monitored. The possibility of preventing the immune response toward the vector was investigated using a rapamycin-based regimen with daily intraperitoneal (i.p.) injections starting 2 days before and ending 21 days after vector administration. In rats treated at postnatal day 1 (P1) or P14, the correction was (partially) lost after 12 weeks, whereas the correction was stable in rats injected at P28. Combining initial vector administration with the immune-suppressive regimen prevented induction of NAbs in female rats, allowing at least partially effective re-administration. Induction of NAbs upon re-injection could not be prevented, suggesting that this strategy will be ineffective in patients with low levels of preexisting anti-AAV NAbs., Graphical Abstract, At postnatal day 28, AAV-hUGT1A1 establishes persistent correction of hyperbilirubinemia in Ugt1a1 deficient rats while earlier treatment results in (partial) loss of efficacy overtime. Only in naive animals does immune suppression by rapamycin effectively bloc NAb induction, allowing effective re-treatment. In primed animals, this induction was reduced but not completely prevented.

MicroRNA (miRNA) expression is a dynamic process in the cell, and the proper time period for post-transcriptional regulation might be critical due to the gene-on/-off expression times of the cell. Here, we investigated the effect of different time-points on proliferation, invasion and miRNA expression profiles of human breast cancer cell lines MCF-7 (non-metastatic, epithelium-like breast cancer cell line with oestrogen receptor (ER) positive (+) and human breast cancer cell lines MDA-MB-435 (metastatic, invasive, ER negative (-). For this purpose, MCF-7 and MDA-MB-435 cells were seeded different number in E-plate 16 for proliferation experiment using an electrical impedance-based real-time cell analyzer system (RTCA) for 168 h. Similarly, invasion potential of MCF-7 and MDA-MB-435 were determined by RTCA for 90 h. Total RNAs including miRNAs were isolated at 2, 4, 6, 12, 24, 48 h from the MCF-7 and MDA-MB-435 cells. Afterward, the quantitative 84 miRNA expressions of MCF-7 and MDA-MB-435 were analyzed by Fluidigm Microfluidic 96.96 Dynamic Array. The results of these study demonstrated that both proliferation potential and invasion capacity of MDA-MB-435 is higher than MCF-7 as time-dependent manner. Furthermore, we detected that up/down expressions of 32 miRNAs at all time points in MDA-MB-435 compared to MCF-7 (at least ten-fold increased). Because of the high number of miRNAs, we more closely evaluated the expression of six of them (miR-100–5p, miR-29a-3p, miR-130a-3p, miR-10a-5p, miR-10b-5p, miR-203a), and determined that their levels were dramatically changed by at least 50-fold at different time points of the experiment (p

Background Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Glutathione-S-methyl transferase (GSTs) enzymes’ family is known to catalyze carcinogens detoxification. Overexpression of (GSTO) omega class was reported in cancer occurrence. The purpose of the study was to investigate the association of GSTO1*A140D (rs4925) and GSTO2*N142D (rs156697) polymorphisms with the susceptibility to childhood ALL and to evaluate their prognostic impact. Genotyping was performed using polymerase chain reaction-restriction fragment length polymorphism technique in 96 Egyptian pediatric ALL patients and 99 controls. Results No statistically significant different GSTO1*A140D genotype and allele distribution was observed among ALL cases and controls; however, a statistically significant different GSTO1*A140D genotype distribution was found between de novo ALL cases and controls [CC (37% vs. 56.6%), CA (47.8% vs. 40.4%), and AA (15.2% vs. 3.0%), respectively] (0.008). GSTO1*A140D variant genotypes’ frequency was significantly higher in de novo cases than in controls (63% vs. 43.4%) (0.028). The minor allele frequency (MAF) of GSTO1*A140D-A was significantly higher in de novo cases compared to controls (0.39 vs. 0.23) (0.005). Genotyping of GSTO2*N142D revealed a statistically significant difference of genotype distribution between ALL patients and controls [AA (26% vs. 36.3%), AG (62.5% vs. 61.6%), and GG (11.4% vs. 2.0%), respectively] (0.017) and between de novo ALL cases and controls [AA (37% vs. 36.3%), AG (45.7% vs. 61.6%), and GG (17.3% vs. 2.0%), respectively] (0.002). The MAF of GSTO2*N142D-G was significantly higher in ALL patients than in controls (0.42 vs. 0.32) (0.046). The high-risk ALL group had a higher frequency of GSTO1*A140D and GSTO2*N142D variant genotypes compared to corresponding wild genotypes and a higher frequency of combined polymorphisms compared to single polymorphisms and wild genotypes but with no statistically significant difference. Conclusion A statistically significant difference of GSTO1*A140D and GSTO2*N142D genotype distribution was detected between de novo ALL cases and controls. Compared to the control group, the MAF of GSTO1*A140D-A was overexpressed in de novo ALL cases and that of GSTO2*N142D-G was significantly higher in ALL patients. These findings suggest that the studied polymorphisms might play a significant role in the susceptibility to de novo childhood ALL in Egypt; however, GSTO1*A140D and/or GSTO2*N142D polymorphisms have no impact on ALL prognosis.

Edible oil is an important part of the human daily diet, which is popular in the food industry. People are paying increasing attention to the safety of edible oil as flawed oils have caused enormous international losses and posed a huge threat to consumer health issues. Therefore, it is necessary and important to analyze the quality and safety of oil product. In the present study, we particularly reviewed recent literature on analysis of emerging pollutants in edible oil including mycotoxins, pesticide residues and heavy metals. In addition, a series of emerging analytical technologies (HPLC, LC-MS/MS and GC-MS) for these contaminants were also summarized in this paper.

Background MicroRNAs play an important role in many fundamental biological and pathological processes. Defining the microRNAs profile underlying the processes by beneficial and detrimental lifestyles, including caloric restriction (CR), exercise and high-fat diet (HF), is necessary for understanding both normal physiology and the pathogenesis of metabolic disease. We used the microarray to detect microRNAs expression in livers from CR, EX and HF mice models. After predicted potential target genes of differentially expressed microRNAs with four algorithms, we applied GO and KEGG to analyze the function of predicted microRNA targets. Results We describe the overall microRNAs expression pattern, and identified 84 differentially expressed microRNAs changed by one or two or even all the three lifestyle modifications. The common and different enriched categories of gene function and main biochemical and signal transduction pathways were presented. Conclusions We provided for the first time a comprehensive and thorough comparison of microRNAs expression profiles in liver among these lifestyle modifications. With this knowledge, our findings provide us with an overall vision of microRNAs in the molecular impact of lifestyle on health as well as useful clues for future and thorough research of the role of microRNAs.

Introduction Blinatumomab, a bi-specific T cell engager (BiTE®) combining the VH and VL domains of two antibodies against human CD19 and CD3, has been approved by U.S. Food and Drug Administration (FDA) for the treatment of patients with relapsed or refractory B precursor ALL (r/r B-ALL) for its clinical benefit demonstrated in different clinical trials. Clinical trials have also shown that there are still patients refractory to blinatumomab. It is thus important to understand the resistance mechanisms. Blinatumomab connects patients' autologous T cells and target cells to form immunologic synapse which potently triggers the activation signaling cascades in T cells and guides T cells to recognize and induce perforin/granzyme-mediated lysis of CD19+ B-ALL cells. Previous studies showed blinatumomab-mediated cytotoxicity involves different T cell subpopulations. But response of each T cell subpopulation to blinatumomab treatment remained largely unknown. Methods and Results In this study, we used 10X Genomics based single cell RNA sequencing to analyze the transcriptome of single T cells before and after blinatumomab treatment. First, ex vivo blinatumomab cytotoxicity model was established, in which healthy PBMCs were used as effector cells and cocultured with target cells (RS4;11 cells or SUP-B15 cells) at an effector-to-target cell ratio of 10:1 with 0.1 ng/mL blinatumomab. Then, PBMCs and BMMCs from 2 B-ALL patients were cultured with 10 ng/mL blinatumomab. Cells from both ex vivo model and patient samples were sequenced using 10X Genomics platform. In total, transcriptome of 17920 single T cells from the ex vivo model and 2271 single T cells from patient sample were analyzed. Based on T cell trajectory analysis, we identified four distinct populations of blinatumomab-activated T cells, which were derived from CD8+ effector memory T (TEM) cells, CD4+ central memory (TCM) cells, naïve T cells and Tregs, respectively. The differentially expressed genes in activated clusters were analyzed to reflect T cell activation mechanisms. The result showed blinatumomab induced the upregulation of aerobic glycolysis pathway (PKM, PGAM1, ENO1, GAPDH and LDHA), cytoskeleton dynamics pathway (ACTD1, ACTB, NME1 and TUBA1B), IFN-responsive pathway (GBP1, PSME2, WARS, CXCL10 and STAT1), and the upregulation of well-known immune-related genes (TNFRSF4, TNFRSF18, LAG3, CD69, IL2RA, MIR155HG, BATF, SH2D2A, LTA, NFKBIA and NDFIP2). We found blinatumomab-activated CD8+ TEM cells showed stronger cytotoxic capability than other activated populations with specific production of cytotoxic factors (PRF1, IFNG and FASLG) and cytokines (CCL2, CCL3, CCL3L1, CCL4, CCL4L2, CCL8, XCL1, XCL2, TNFSF9 and TNFSF14). Last, differential gene expression analysis revealed that co-stimulatory (TNFRSF4,TNFRSF9 and TNFRSF18) and co-inhibitory receptors (LAG3 and TIGIT) were similarly up-regulated in clusters activated from memory and naïve T cells, indicating ligand dependent T cell functional outcomes induced by blinatumomab. Conclusion In summary, we used single cell sequencing to map the blinatumomab-mediated T cell activation state transition and reveal the molecular changes in different T cell subpopulations. Memory T cells, naïve T cells and Tregs were identified functional populations after blinatumomab treatment. CD8+ TEM accounted for the majority of blinatumomab-induced cytotoxicity. Furthermore, T cell co-regulatory receptors were identified as potential targets accountable for blinatumomab sensitivity or resistance mechanisms. The study demonstrated that the collected cellular transcriptional profiles can serve as resource to explore novel strategies to enhance the efficacy of blinatumomab. Disclosures Yin: Amgen: Employment. Huo:Amgen: Employment. Sheng:Amgen: Employment. Li:Amgen: Employment. Ellwanger:Amgen: Employment. Lu:Amgen: Employment. Homann:Amgen: Employment. Wang:Amgen: Employment. Ren:Ruijin hospital: Employment.

Background This article presents the results of long-term observations and comparative analysis of genotype–phenotype features in a large group of patients (227 males and one female) with a severe, intermediate and mild form of Hunter syndrome, evaluating the quality and span of their lives, as well as their ability to social adaptation. Methods We used electrophoresis of glycosaminoglycans of urine, determination of the activity of lysosomal enzymes in plasma, in dried blood spots according to the generally accepted method and DNA analysis. Results The clinical symptomatology of 228 patients with Hunter syndrome was characterized by growth retardation, lesions of the bronchopulmonary, cardiovascular, nervous systems, etc. Thirty-five patients had an attenuated form of the disease. DNA was available from all patients. 19 patients from 10 families had a mild form of the disease. 42 patients from 41 families had an intermediate form of the disease. All other patients had a severe form of the disease. We provide brief clinical examples of some patients with a mild form of Hunter syndrome. Currently, 113 patients with Hunter syndrome receive enzyme replacement therapy (idursulfase or idursulfase beta). Conclusion The long-term study of the large number of patients with Hunter syndrome helped identify disease-associated variants leading to severe and mild forms of the disease. The treatment effect and successful social adaptation of patients with a mild form of Hunter syndrome were revealed.

Susana Seixas,1,2 Patricia Isabel Marques1,2 1i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; 2Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, PortugalCorrespondence: Susana Seixasi3S, Rua Alfredo Allen, 208, Porto, 4200-135, PortugalTel +351 220408806Email sseixas@ipatimup.ptAbstract: Alpha-1-Antitrypsin deficiency (AATD), caused by SERPINA1 mutations, is one of the most prevalent Mendelian disorders among individuals of European descend. However, this condition, which is characterized by reduced serum levels of alpha-1-antitrypsin (AAT) and associated with increased risks of pulmonary emphysema and liver disease in both children and adults, remains frequently underdiagnosed. AATD clinical manifestations are often correlated with two pathogenic variants, the Z allele (p.Glu342Lys) and the S allele (p.Glu264Val), which can be combined in severe ZZ or moderate SZ risk genotypes. Yet, screenings of AATD cases and large sequencing efforts carried out in both control and disease populations are disclosing outstanding numbers of rare SERPINA1 variants (> 500), including many pathogenic and other likely deleterious mutations. Generally speaking, pathogenic variants can be subdivided into either loss- or gain-of-function according to their pathophysiological effects. In AATD, the loss-of-function is correlated with an uncontrolled activity of elastase by its natural inhibitor, the AAT. This phenomenon can result from the absence of circulating AAT (null alleles), poor AAT secretion from hepatocytes (deficiency alleles) or even from a modified inhibitory activity (dysfunctional alleles). On the other hand, the gain-of-function is connected with the formation of AAT polymers and their switching on of cellular stress and inflammatory responses (deficiency alleles). Less frequently, the gain-of-function is related to a modified protease affinity (dysfunctional alleles). Here, we revisit SERPINA1 mutation spectrum, its origins and population history with a greater emphasis on variants fitting the aforementioned processes of AATD pathogenesis. Those were selected based on their clinical significance and wider geographic distribution. Moreover, we also provide some directions for future studies of AATD clinically heterogeneity and comprehensive diagnosis.Keywords: SERPINA1 variants, Z allele, S allele, MMalton allele and QOurém allele

Single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) identifies regulated chromatin accessibility modules at the single-cell resolution. Robust evaluation is critical to the development of scATAC-seq pipelines, which calls for reproducible datasets for benchmarking. We hereby present the simATAC framework, an R package that generates scATAC-seq count matrices that highly resemble real scATAC-seq datasets in library size, sparsity, and chromatin accessibility signals. simATAC deploys statistical models derived from analyzing 90 real scATAC-seq cell groups. simATAC provides a robust and systematic approach to generate in silico scATAC-seq samples with known cell labels for assessing analytical pipelines. Supplementary Information The online version contains supplementary material available at (10.1186/s13059-021-02270-w).

As an important quality control link of molecular diagnosis, genetic reference materials (RMs) are widely used in various gene detection platforms such as mutation detection, gene quantification, and second generation sequencing. However, contamination, construction, and storage of existing genetic RMs still remain challenges. Here, we established a new genetic RM system based on Saccharomyces cerevisiae. We chose the non-small cell lung cancer (NSCLC) mutation hotspots in Kirsten rat sarcoma viral oncogene (KRAS) and epidermal growth factor receptor (EGFR), using clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas9) system-mediated gene editing technology, combined with the high homologous recombination efficiency of Saccharomyces cerevisiae. A single copy of the target gene was inserted into the yeast genome, and the inserted target gene was stably inherited with the passage of yeast cells. The copy number calculation for the target gene can replays by cell counting. The RM system was evaluated by sequence, copy number, stability, and homogeneity. In summary, the recombinant yeast cell line has ease of construction and screening, stable genetic characteristics, accurate copy number calculation, and convenient culture and preservation. Our findings may provide new ideas and directions for the research and industrialization of genetic RMs.

KCS (3-ketoacyl-CoA synthase) is the key enzyme catalyzing the first step of very long chain fatty acid (VLCFA) biosynthesis. Studies showed that different KCSs possessed different substrate preference. Malania oleifera are abundance of VLCFAs in its mature seeds, especially the nervonic acid, which is essential for human health. In this study, we identified and characterized 18 KCS genes in M. oleifera genome. Phylogenetic analysis showed that these KCS genes were classified into four subfamilies, including two FAE-like, six KCS-like, eight FDH-like and two CER6. We concentrated on the functional role of two FAE-like genes, Maole003085.T1 and Maole004215.T1 which encoded predicted amino acid residues of 516 and 518 in protein, respectively. Multiple sequence alignment showed that their two proteins contained the known and conserved active sites among FAE-like subfamily. Upon heterologous expression in wild type yeast (Saccharomyces cerevisiae) INVSc1, we found that Maole004215.T1 could produce four new fatty acids including C22:0/C22:1 and C24:0/C24:1, but Maole003085.T1 only produced C22:1. Besides, upon heterologous expression in mutant yeast BY4741-△elo3, we found the Maole003085.T1 could produce C24:0 and C26:0, while the Maole004215.T1 could catalyze the formation of fatty acids C24:0, C26:0 and C28:0. These results showed Maole003085.T1 and Maole004215.T1 had fatty acid elongation activity in yeast, and possessed different substrate preference in the production of different VLCFAs. Interestingly, we found Maole004215.T1 could produce nervonic acid in yeast, which provides molecular basis on the genetic improvement and genic engineering for producing nervonic acid resources by using biotechnological methods.

BackgroundNewborn screening aims to identify individual patients who could benefit from early management, treatment, and/or surveillance practices. As sequencing technologies have progressed and we move into the era of precision medicine, genomic sequencing has been introduced to this area with the hopes of detecting variants related to a vastly expanded number of conditions. Though implementation of genomic sequencing for newborn screening in public health and clinical settings is limited, commercial laboratories have begun to offer genomic screening panels for neonates.MethodsWe examined genes listed on four commercial laboratory genomic screening panels for neonates and assessed their clinical actionability using an established age-based semi-quantitative metric to categorize them. We identified genes that were included on multiple panels or distinct between panels.ResultsThree hundred and nine genes appeared on one or more commercial panels: 74 (23.9%) genes were included in all four commercial panels, 45 (14.6%) were on only three panels, 76 (24.6%) were on only two panels, and 114 (36.9%) genes were listed on only one of the four panels. Eighty-two genes (26.5%) listed on one or more panels were assessed by our method to be inappropriate for newborn screening and to require additional parental decision-making. Conversely, 249 genes that we previously identified as being highly actionable were not listed on any of the four commercial laboratory genomic screening panels.ConclusionsCommercial neonatal genomic screening panels have heterogeneous content and may contain some conditions with lower actionability than would be expected for public health newborn screening; conversely, some conditions with higher actionability may be omitted from these panels. The lack of transparency about how conditions are selected suggests a need for greater detail about panel content in order for parents to make informed decisions. The nuanced activity of gene list selection for genomic screening should be iteratively refined with evidence-based approaches to provide maximal benefit and minimal harm to newborns.

Novel vaccines are required to effectively combat the epidemic spread of tuberculosis. Using in silico approaches, this study focuses on prediction of potential B cell and T cell binding immunogenic epitopes for 30 putative outer membrane proteins of Mtb. Among these, certain immunodominant epitopes of Rv0172, Rv0295c, Rv1006, Rv2264c, and Rv2525c were found, which are capable of binding B-cell and a maximum number of MHC alleles. The selected immunodominant epitopes were screened for their allergenic and antigenic properties, their percentage identity against the human proteome and their structural properties. Further, the binding efficacy of the immunodominant epitopes of Rv0295c and Rv1006 with HLA-DRB1*04:01 was analyzed using molecular docking and molecular dynamics studies. Hence, the in silico-derived immunogenic peptides (epitopes) could potentially be used for the design of subunit vaccines against tuberculosis. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-021-00148-9.

Various mitochondrial diseases, including mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS), are associated with heteroplasmic mutations in mitochondrial DNA (mtDNA). Herein, we refined a previously generated G13513A mtDNA-targeted platinum transcription activator-like effector nuclease (G13513A-mpTALEN) to more efficiently manipulate mtDNA heteroplasmy in MELAS-induced pluripotent stem cells (iPSCs). Introduction of a nonconventional TALE array at position 6 in the mpTALEN monomer, which recognizes the sequence around the m.13513G>A position, improved the mpTALEN effect on the heteroplasmic shift. Furthermore, the reduced expression of the new Lv-mpTALEN(PKLB)/R-mpTALEN(PKR6C) pair by modifying codons in their expression vectors could suppress the reduction in the mtDNA copy number, which contributed to the rapid recovery of mtDNA in mpTALEN-applied iPSCs during subsequent culturing. Moreover, MELAS-iPSCs with a high proportion of G13513A mutant mtDNA showed unusual properties of spontaneous, embryoid body-mediated differentiation in vitro, which was relieved by decreasing the heteroplasmy level with G13513A-mpTALEN. Additionally, drug-inducible, myogenic differentiation 1 (MYOD)-transfected MELAS-iPSCs (MyoD-iPSCs) efficiently differentiated into myosin heavy chain-positive myocytes, with or without mutant mtDNA. Hence, heteroplasmic MyoD-iPSCs controlled by fine-tuned mpTALENs may contribute to a detailed analysis of the relationship between mutation load and cellular phenotypes in disease modeling., Graphical Abstract, Yahata et al. refined a previous G13513A-mpTALEN to more efficiently manipulate mtDNA heteroplasmy in MELAS-iPSCs. Mutation-rich MELAS-iPSCs showed unusual differentiation properties, which were recovered by decreasing the heteroplasmy levels with new G13513A-mpTALEN. They further demonstrated that drug-inducible, MYOD-transfected MELAS-iPSCs could efficiently differentiate into MyHC-positive myocytes, with or without mutant mtDNA.

Aspergillus fumigatus is one of the ubiquitous fungi with airborne conidia, which accounts for most aspergillosis cases. In immunocompetent hosts, the inhaled conidia are rapidly eliminated. However, immunocompromised or immunodeficient hosts are particularly vulnerable to most Aspergillus infections and invasive aspergillosis (IA), with mortality from 50% to 95%. Despite the improvement of antifungal drugs over the last few decades, the therapeutic effect for IA patients is still limited and does not provide significant survival benefits. The drawbacks of antifungal drugs such as side effects, antifungal drug resistance, and the high cost of antifungal drugs highlight the importance of finding novel therapeutic and preventive approaches to fight against IA. In this article, we systemically addressed the pathogenic mechanisms, defense mechanisms against A. fumigatus, the immune response, molecular aspects of host evasion, and vaccines’ current development against aspergillosis, particularly those based on AFMP4 protein, which might be a promising antigen for the development of anti-A. fumigatus vaccines.

Systemic or localized application of glucocorticoids (GCs) can lead to iatrogenic ocular hypertension, which is a leading cause of secondary open-angle glaucoma and visual impairment. Previous work has shown that dexamethasone increases zonula occludens-1 (ZO-1) protein expression in trabecular meshwork (TM) cells, and that an antisense oligonucleotide inhibitor of ZO-1 can abolish the dexamethasone-induced increase in trans-endothelial flow resistance in cultured Schlemm’s canal (SC) endothelial and TM cells. We have previously shown that intracameral inoculation of small interfering RNA (siRNA) targeting SC endothelial cell tight junction components, ZO-1 and tricellulin, increases aqueous humor outflow facility ex vivo in normotensive mice by reversibly opening SC endothelial paracellular pores. In this study, we show that targeted siRNA downregulation of these SC endothelial tight junctions reduces intraocular pressure (IOP) in vivo, with a concomitant increase in conventional outflow facility in a well-characterized chronic steroid-induced mouse model of ocular hypertension, thus representing a potential focused clinical application for this therapy in a sight-threatening scenario., Graphical Abstract, Cassidy and colleagues show that intracameral inoculation of siRNA targeting Schlemm’s canal endothelial cell tight junction proteins, ZO-1 and tricellulin, can reduce intraocular pressure and increase outflow facility in a murine model of steroid-induced ocular hypertension.

Staphylococci are among the most frequent human microbiota components associated with the high level of bloodstream infection (BSI) episodes. In predisposed patients, there is a high risk of transformation of BSI episodes to sepsis. Both bacterial and host factors are crucial for the outcomes of BSI and sepsis. The highest rates of BSI episodes were reported in Africa, where these infections were up to twice as high as the European rates. However, there remains a great need to analyze African data for comprehensive quantification of staphylococcal BSI prevalence. The lowest rates of BSI exist in Australia. Asian, European, and North American data showed similar frequency values. Worldwide analysis indicated that both Staphylococcus aureus and coagulase-negative staphylococci (CoNS) are the most frequent BSI agents. In the second group, the most prevalent species was Staphylococcus epidermidis, although CoNS were not identified at the species level in many studies. The lack of a significant worldwide decrease in BSI episodes indicates a great need to implement standardized diagnostic methods and research etiological factors using advanced genetic methods.

Introduction Nonaccidental trauma (NAT) is considered when pediatric patients present with intracranial injuries and a negative history of an accidental injury or concomitant medical diagnosis. The evaluation of NAT should include the consideration of possible medical causes including coagulation, hematologic, metabolic and other genetic disorders, as well as witnessed and unwitnessed accidental injuries. Case Presentation We present a 7‐month‐old male with spells and incidental findings of bilateral subdural hematomas, retinal hemorrhages, and secondary macrocephaly, leading to investigation for NAT. Biochemical analysis showed excretion of a large amount of D‐2‐hydroxyglutaric in urine consistent with a biochemical diagnosis of D‐2‐hydroxyglutaric aciduria, a rare neurometabolic disorder characterized by developmental delay, epilepsy, hypotonia, and psychomotor retardation. None of these symptoms were present in our patient at the time of diagnosis. Molecular genetic testing revealed a pathogenic splice site variant (c.685‐2A>G) and a variant of uncertain significance (c.1256G>T) with evidence of pathogenicity in the D2HGDH gene, consistent with a molecular diagnosis of D‐2‐hydroxyglutaric aciduria type I (OMIM #600721). Conclusion Since several metabolic disorders, including D‐2‐hydroxyglutaric aciduria type I, can present solely with symptoms suggestive of NAT (subdural and retinal hemorrhages), an early metabolic evaluation by urine organic acid analysis should be included in clinical protocols evaluating NAT. A methodical and nonjudgmental approach coordinated between pediatricians and metabolic specialists is also necessary to ensure that rare genetic conditions are not overlooked to prevent devastating social, legal, and financial consequences of suspected child abuse.

Exosome-derived microRNAs (miRNAs) are potential diagnostic biomarkers. However, little is known about their effectiveness as diagnostic biomarkers of fulminant myocarditis (FM). This study aimed to explore serum exosomal miRNAs as potential biomarkers for FM diagnosis. Peripheral blood samples were collected from 99 patients with FM, 32 patients with nonfulminant myocarditis (NFM), and 105 healthy controls (HCs). The miRNA expression profiles of serum exosomes were determined using next-generation sequencing, and differentially expressed miRNAs were further analyzed by quantitative reverse transcriptase polymerase chain reaction. A logistic regression model was constructed using a training cohort (n = 120) and then validated using an independent cohort (n = 106). The area under the receiver operating characteristic curve was used to evaluate diagnostic accuracy. In FM patients, hsa-miR-30a, hsa-miR-192, hsa-miR-146a, hsa-miR-155, and hsa-miR-320a were validated as significantly and differentially expressed candidates that could serve as potential markers for diagnosing FM. In addition, the miRNA panel (hsa-miR-155 and hsa-miR-320a) from the multivariate logistic regression model demonstrated high accuracy in the diagnosis of FM and was able to distinguish FM from HCs and NFM. Moreover, the diagnostic value of the miRNA panel was greater than that of CRP and cTn alone or together. The miRNA panel provided the excellent diagnostic capability for FM., Graphical Abstract, This study investigated the exosome-derived miRNA profiles in serum from patients with FM and found that the miRNA panel for FM diagnosis exhibited high accuracy in distinguishing FM from HCs and NFM. Our results support the hypothesis that circulating exosomal miRNA profiles can serve as noninvasive biomarkers of FM.

Background K-mer-based methods have greatly advanced in recent years, largely driven by the realization of their biological significance and by the advent of next-generation sequencing. Their speed and their independence from the annotation process are major advantages. Their utility in the study of the mobilome has recently emerged and they seem a priori adapted to the patchy gene distribution and the lack of universal marker genes of viruses and plasmids. To provide a framework for the interpretation of results from k-mer based methods applied to archaea or their mobilome, we analyzed the 5-mer DNA profiles of close to 600 archaeal cells, viruses and plasmids. Archaea is one of the three domains of life. Archaea seem enriched in extremophiles and are associated with a high diversity of viral and plasmid families, many of which are specific to this domain. We explored the dataset structure by multivariate and statistical analyses, seeking to identify the underlying factors. Results For cells, the 5-mer profiles were inconsistent with the phylogeny of archaea. At a finer taxonomic level, the influence of the taxonomy and the environmental constraints on 5-mer profiles was very strong. These two factors were interdependent to a significant extent, and the respective weights of their contributions varied according to the clade. A convergent adaptation was observed for the class Halobacteria, for which a strong 5-mer signature was identified. For mobile elements, coevolution with the host had a clear influence on their 5-mer profile. This enabled us to identify one previously known and one new case of recent host transfer based on the atypical composition of the mobile elements involved. Beyond the effect of coevolution, extrachromosomal elements strikingly retain the specific imprint of their own viral or plasmid taxonomic family in their 5-mer profile. Conclusion This specific imprint confirms that the evolution of extrachromosomal elements is driven by multiple parameters and is not restricted to host adaptation. In addition, we detected only recent host transfer events, suggesting the fast evolution of short k-mer profiles. This calls for caution when using k-mers for host prediction, metagenomic binning or phylogenetic reconstruction.

Background Stauntonia chinensis DC. belongs to subfamily Lardizabaloideae, which is widely grown throughout southern China. It has been used as a traditional herbal medicinal plant, which could synthesize a number of triterpenoid saponins with anticancer and anti-inflammatory activities. However, the wild resources of this species and its relatives were threatened by over-exploitation before the genetic diversity and evolutionary analysis were uncovered. Thus, the complete chloroplast genome sequences of Stauntonia chinensis and comparative analysis of chloroplast genomes of Lardizabaloideae species are necessary and crucial to understand the plastome evolution of this subfamily. Results A series of analyses including genome structure, GC content, repeat structure, SSR component, nucleotide diversity and codon usage were performed by comparing chloroplast genomes of Stauntonia chinensis and its relatives. Although the chloroplast genomes of eight Lardizabaloideae plants were evolutionary conserved, the comparative analysis also showed several variation hotspots, which were considered as highly variable regions. Additionally, pairwise Ka/Ks analysis showed that most of the chloroplast genes of Lardizabaloideae species underwent purifying selection, whereas 25 chloroplast protein coding genes were identified with positive selection in this subfamily species by using branch-site model. Bayesian and ML phylogeny on CCG (complete chloroplast genome) and CDs (coding DNA sequences) produced a well-resolved phylogeny of Lardizabaloideae plastid lineages. Conclusions This study enhanced the understanding of the evolution of Lardizabaloideae and its relatives. All the obtained genetic resources will facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of subfamily Lardizabaloideae.

Discovery of non-coding RNAs has paradigmatically shifted our understanding of the multifaceted nature of cancer. It is becoming progressively more understandable that long non-coding RNAs play fundamental role in regulation of cell signaling pathways in different cancers. DANCR has started to gain remarkable appreciation because of its central role in cancer onset and progression. In this review we have attempted to summarize emerging aspects of DANCR-mediated regulation of Wnt/β-catenin and JAK/STAT pathways in different cancers. We have also discussed how DANCR epigenetically inactivated tumor suppressors to promote cancer. There is sufficient experimental evidence related to oncogenic role of DANCR in variety of cancers. However, there is a need to uncover how DANCR modulates various other oncogenic pathways in different cancers.

Background Safety issues of probiotic products have been reported frequently in recent years. Ten bacterial strains isolated from seven commercial probiotic products on market were evaluated for their safety, by whole-genome analysis. Results We found that the bacterial species of three probiotic products were incorrectly labeled. Furthermore, six probiotic product isolates (PPS) contained genes for the production of toxic metabolites, while another three strains contained virulence genes, which might pose a potential health risk. In addition, three of them have drug-resistance genes, among which two strains potentially displayed multidrug resistance. One isolate has in silico predicted transferable genes responsible for toxic metabolite production, and they could potentially transfer to human gut microflora or environmental bacteria. Isolates of Lactobacillus rhamnosus and Bifidobacterium animalis subsp. lactis are associated with low risk for human consumption. Based on a comparative genome analysis, we found that the isolated Enterococcus faecium TK-P5D clustered with a well-defined probiotic strain, while E. faecalis TK-P4B clustered with a pathogenic strain. Conclusions Our work clearly illustrates that whole-genome analysis is a useful method to evaluate the quality and safety of probiotic products. Regulatory quality control and stringent regulations on probiotic products are needed to ensure safe consumption and protect human health.

Waseem Chauhan,1 Mohammad Afzal,1 Zeeba Zaka-ur-Rab,2 Md Salik Noorani3 1Department of Zoology, Aligarh Muslim University, Aligarh, India; 2Department of Pediatrics, Jawahar Lal Nehru Medical College, Aligarh Muslim University, Aligarh, India; 3Department of Botany, Jamia Hamdard, New Delhi, IndiaCorrespondence: Mohammad AfzalHuman Genetics and Toxicology Laboratory, Department of Zoology, Aligarh Muslim University, Aligarh, IndiaTel +919897839601Email afzal1235@rediffmail.comPurpose: Beta thalassemia is one of the most common inherited disorders in India with heterogenous clinical phenotypes from silent carrier to clinically severe ones. Our study aimed to characterize the mutation spectrum in thalassemia patients who are coming to the hospital for follow-up from the western region of Uttar Pradesh India.Patients and Methods: For the study, a case series of the retrospective bi-centre study was conducted. The patients from two thalassemia centers in the major hospitals (LLRMC Meerut, and JNMC, Aligarh administered by the Ministry of Health and Family Welfare (MoHFW)) in the Western Uttar Pradesh, India were considered for the study. A total of 77 blood samples were obtained from individuals (both related and unrelated) diagnosed with β-thalassemia after their consent. After DNA extraction, HBB gene amplification, mutation-specific polymerase chain reaction and gene sequencing were carried out to analyze the mutations.Results: In this study, seven different types of mutations were reported for the first time in Western Uttar Pradesh, India. A novel frameshift mutation, deletion of 4 nucleotides Codon 66/67 (-AAAG) in exon 2 region, is reported for the first time. IVS 1– 5 (G>C) and Codon 41/42 (-CTTT) are the most frequently reported mutations. The molecular spectrum for these two cases consists of 44 and 42 alleles out of 108 alleles, respectively.Conclusion: A total of 108 β-thalassemia alleles were studied from 46 homozygous and 31 compound heterozygous patients. All the individuals were from 20 districts of the Western Uttar Pradesh, India.Keywords: codon 41/42-CTTT, IVS I-5G>C, beta globin, mutation, beta-thalassemia major

Human induced pluripotent stem cell-derived intestinal epithelial cells (hiPSC-IECs) are expected to be utilized in regenerative medicine. To perform a safe transplantation without the risk of tumor formation, residual undifferentiated hiPSCs must be removed from hiPSC-IECs. In this study, we examined whether vinblastine (a multiple drug resistance 1 [MDR1] substrate) could remove residual undifferentiated hiPSCs in hiPSC-IECs and attempted to generate hiPSC-IECs applicable to transplantation medicine. We found that the expression levels of pluripotent markers were largely decreased and those of intestinal markers were increased by vinblastine treatment. The treatment of undifferentiated hiPSCs with vinblastine significantly decreased their viability. These results suggested that undifferentiated hiPSCs can be eliminated from hiPSC-IECs by vinblastine treatment. We hypothesized that MDR1-negative cells (such as undifferentiated hiPSCs) die upon vinblastine treatment because they are unable to excrete vinblastine. As expected, the cell viability of MDR1-knockout hiPSC-IECs was significantly decreased by vinblastine treatment. Furthermore, teratomas were formed by subcutaneous transplantation of hiPSC-IECs mixed with undifferentiated hiPSCs into mice, but they were not observed when the transplanted cells were pre-treated with vinblastine. Vinblastine-treated hiPSC-IECs would be an effective cell source for safe regenerative medicine., Graphical Abstract, This study showed that vinblastine (a multiple drug resistance 1 substrate) can remove residual undifferentiated human induced pluripotent stem cells (hiPSCs) in hiPSC-derived intestinal epithelial cells (hiPSC-IECs) and enhances the functions of hiPSC-IECs. Vinblastine-treated hiPSC-IECs would be an effective cell source for safe regenerative medicine.

Background The red swamp crayfish Procambarus clarkii is a freshwater species that possesses high adaptability, environmental tolerance, and fecundity. P. clarkii is artificially farmed on a large scale in China. However, the molecular mechanisms of ovarian development in P. clarkii remain largely unknown. In this study, we identified four stages of P. clarkii ovary development, the previtellogenic stage (stage I), early vitellogenic stage (stage II), middle vitellogenic stage (stage III), and mature stage (stage IV) and compared the transcriptomics among these four stages through next-generation sequencing (NGS). Results The total numbers of clean reads of the four stages ranged from 42,013,648 to 62,220,956. A total of 216,444 unigenes were obtained, and the GC content of most unigenes was slightly less than the AT content. Principal Component Analysis (PCA) and Anosim analysis demonstrated that the grouping of these four stages was feasible, and each stage could be distinguished from the others. In the expression pattern analysis, 2301 genes were continuously increase from stage I to stage IV, and 2660 genes were sharply decrease at stage IV compared to stages I-III. By comparing each of the stages at the same time, four clusters of differentially expressed genes (DEGs) were found to be uniquely highly expressed in stage I (136 genes), stage II (43 genes), stage III-IV (49 genes), and stage IV (22 genes), thus exhibiting developmental stage specificity. Moreover, in comparisons between adjacent stages, the number of DEGs between stage III and IV was the highest. GO enrichment analysis demonstrated that nutrient reservoir activity was highest at stage II and that this played a foreshadowing role in ovarian development, and the GO terms of cell, intracellular and organelle participated in the ovary maturation during later stages. In addition, KEGG pathway analysis revealed that the early development of the ovary was mainly associated with the PI3K-Akt signaling pathway and focal adhesion; the middle developmental period was related to apoptosis, lysine biosynthesis, and the NF-kappa B signaling pathway; the late developmental period was involved with the cell cycle and the p53 signaling pathway. Conclusion These transcriptomic data provide insights into the molecular mechanisms of ovarian development in P. clarkii. The results will be helpful for improving the reproduction and development of this aquatic species.

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an important bacterium of nosocomial infections. In this study, CRKP strains, which were mainly isolated from fecal samples of 14 patients in three wards of the hospital in the Silesia Voivodship, rapidly increased from February to August 2018. Therefore, we conducted microbiological and molecular studies of the CRKP isolates analyzed. Colonized patients had critical underlying diseases and comorbidities; one developed bloodstream infection, and five died (33.3%). Antibiotic susceptibilities were determined by the E-test method. A disc synergy test confirmed carbapenemase production. CTX-Mplex PCR evaluated the presence of resistance genes bla CTX-M-type, bla CTX-M-1, bla CTX-M-9, and the genes bla SHV, bla TEM, bla KPC-2, bla NDM-1, bla OXA-48, bla IMP, and bla VIM-1 was detected with the PCR method. Clonality was evaluated by Multi Locus Sequence Typing (MLST) and Pulsed Field Gel Electrophoresis (PFGE). Six (40%) strains were of XDR (Extensively Drug-Resistant) phenotype, and nine (60%) of the isolates exhibited MDR (Multidrug-Resistant) phenotype. The range of carbapenem minimal inhibitory concentrations (MICs, μg/mL) was as follows doripenem (16 to >32), ertapenem (> 32), imipenem (4 to > 32), and meropenem (> 32). PCR and sequencing confirmed the bla CTX-M-15, bla KPC-2, bla OXA-48, and bla VIM-1 genes in all strains. The isolates formed one large PFGE cluster (clone A). MLST assigned them to the emerging high-risk clone of ST147 (CC147) pandemic lineage harboring the bla OXA-48 gene. This study showed that the K. pneumoniae isolates detected in the multi-profile medical centre in Katowice represented a single strain of the microorganism spreading in the hospital environment.

Background Suaeda glauca (S. glauca) is a halophyte widely distributed in saline and sandy beaches, with strong saline-alkali tolerance. It is also admired as a landscape plant with high development prospects and scientific research value. The S. glauca chloroplast (cp) genome has recently been reported; however, the mitochondria (mt) genome is still unexplored. Results The mt genome of S. glauca were assembled based on the reads from Pacbio and Illumina sequencing platforms. The circular mt genome of S. glauca has a length of 474,330 bp. The base composition of the S. glauca mt genome showed A (28.00%), T (27.93%), C (21.62%), and G (22.45%). S. glauca mt genome contains 61 genes, including 27 protein-coding genes, 29 tRNA genes, and 5 rRNA genes. The sequence repeats, RNA editing, and gene migration from cp to mt were observed in S. glauca mt genome. Phylogenetic analysis based on the mt genomes of S. glauca and other 28 taxa reflects an exact evolutionary and taxonomic status of S. glauca. Furthermore, the investigation on mt genome characteristics, including genome size, GC contents, genome organization, and gene repeats of S. gulaca genome, was investigated compared to other land plants, indicating the variation of the mt genome in plants. However, the subsequently Ka/Ks analysis revealed that most of the protein-coding genes in mt genome had undergone negative selections, reflecting the importance of those genes in the mt genomes. Conclusions In this study, we reported the mt genome assembly and annotation of a halophytic model plant S. glauca. The subsequent analysis provided us a comprehensive understanding of the S. glauca mt genome, which might facilitate the research on the salt-tolerant plant species.

BackgroundOver the past decade, Fourier transform infrared (FTIR) spectroscopy has been used to predict novel milk protein phenotypes. Genomic data might help predict these phenotypes when integrated with milk FTIR spectra. The objective of this study was to investigate prediction accuracy for milk protein phenotypes when heterogeneous on-farm, genomic, and pedigree data were integrated with the spectra. To this end, we used the records of 966 Italian Brown Swiss cows with milk FTIR spectra, on-farm information, medium-density genetic markers, and pedigree data. True and total whey protein, and five casein, and two whey protein traits were analyzed. Multiple kernel learning constructed from spectral and genomic (pedigree) relationship matrices and multilayer BayesB assigning separate priors for FTIR and markers were benchmarked against a baseline partial least squares (PLS) regression. Seven combinations of covariates were considered, and their predictive abilities were evaluated by repeated random sub-sampling and herd cross-validations (CV).ResultsAddition of the on-farm effects such as herd, days in milk, and parity to spectral data improved predictions as compared to those obtained using the spectra alone. Integrating genomics and/or the top three markers with a large effect further enhanced the predictions. Pedigree data also improved prediction, but to a lesser extent than genomic data. Multiple kernel learning and multilayer BayesB increased predictive performance, whereas PLS did not. Overall, multilayer BayesB provided better predictions than multiple kernel learning, and lower prediction performance was observed in herd CV compared to repeated random sub-sampling CV.ConclusionsIntegration of genomic information with milk FTIR spectral can enhance milk protein trait predictions by 25% and 7% on average for repeated random sub-sampling and herd CV, respectively. Multiple kernel learning and multilayer BayesB outperformed PLS when used to integrate heterogeneous data for phenotypic predictions.