The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild

Background The only known albino gorilla, named Snowflake, was a male wild born individual from Equatorial Guinea who lived at the Barcelona Zoo for almost 40 years. He was diagnosed with non-syndromic oculocutaneous albinism, i.e. white hair, light eyes, pink skin, photophobia and reduced visual acuity. Despite previous efforts to explain the genetic cause, this is still unknown. Here, we study the genetic cause of his albinism and making use of whole genome sequencing data we find a higher inbreeding coefficient compared to other gorillas. Results We successfully identified the causal genetic variant for Snowflake¿s albinism, a non-synonymous single nucleotide variant located in a transmembrane region of SLC45A2. This transporter is known to be involved in oculocutaneous albinism type 4 (OCA4) in humans. We provide experimental evidence that shows that this amino acid replacement alters the membrane spanning capability of this transmembrane region. Finally, we provide a comprehensive study of genome-wide patterns of autozygogosity revealing that Snowflake¿s parents were related, being this the first report of inbreeding in a wild born Western lowland gorilla. Conclusions In this study we demonstrate how the use of whole genome sequencing can be extended to link genotype and phenotype in non-model organisms and it can be a powerful tool in conservation genetics (e.g., inbreeding and genetic diversity) with the expected decrease in sequencing cost. Keywords: Gorilla; Albinism; Inbreeding; Genome; Conservatio

Symposium on the Scottish labour market

In the post-war period, up to the late 1960s, Britain enjoyed a modicum of unemployment and government policies which were geared to producing Full Employment were considered a success. It was simple - boost demand and more people would find work. But the mid 1970s the economic regency enjoyed by those advocating demand sided policies fell into disrepute as the OPEC nations raised prices dramatically and brought in a new era of both rising prices and unemployment. The laws of economics, which previously had viewed policy decisions as the choice between lower unemployment and higher inflation were now redundant. Both unemployment and inflation were moving in the same direction. The era of stagflation had begun

Reconstructing cell cycle and disease progression using deep learning

We show that deep convolutional neural networks combined with nonlinear dimension reduction enable reconstructing biological processes based on raw image data. We demonstrate this by reconstructing the cell cycle of Jurkat cells and disease progression in diabetic retinopathy. In further analysis of Jurkat cells, we detect and separate a subpopulation of dead cells in an unsupervised manner and, in classifying discrete cell cycle stages, we reach a sixfold reduction in error rate compared to a recent approach based on boosting on image features. In contrast to previous methods, deep learning based predictions are fast enough for on-the-fly analysis in an imaging flow cytometer

Gaussian Fluctuations of Eigenvalues in Wigner Random Matrices

We study the fluctuations of eigenvalues from a class of Wigner random matrices that generalize the Gaussian orthogonal ensemble. We begin by considering an $n \times n$ matrix from the Gaussian orthogonal ensemble (GOE) or Gaussian symplectic ensemble (GSE) and let $x_k$ denote eigenvalue number $k$. Under the condition that both $k$ and $n-k$ tend to infinity with $n$, we show that $x_k$ is normally distributed in the limit. We also consider the joint limit distribution of $m$ eigenvalues from the GOE or GSE with similar conditions on the indices. The result is an $m$-dimensional normal distribution. Using a recent universality result by Tao and Vu, we extend our results to a class of Wigner real symmetric matrices with non-Gaussian entries that have an exponentially decaying distribution and whose first four moments match the Gaussian moments.Comment: 21 pages, to appear, J. Stat. Phys. References and other corrections suggested by the referees have been incorporate

ProteinSeq: High-Performance Proteomic Analyses by Proximity Ligation and Next Generation Sequencing

Despite intense interest, methods that provide enhanced sensitivity and specificity in parallel measurements of candidate protein biomarkers in numerous samples have been lacking. We present herein a multiplex proximity ligation assay with readout via realtime PCR or DNA sequencing (ProteinSeq). We demonstrate improved sensitivity over conventional sandwich assays for simultaneous analysis of sets of 35 proteins in 5 µl of blood plasma. Importantly, we observe a minimal tendency to increased background with multiplexing, compared to a sandwich assay, suggesting that higher levels of multiplexing are possible. We used ProteinSeq to analyze proteins in plasma samples from cardiovascular disease (CVD) patient cohorts and matched controls. Three proteins, namely P-selectin, Cystatin-B and Kallikrein-6, were identified as putative diagnostic biomarkers for CVD. The latter two have not been previously reported in the literature and their potential roles must be validated in larger patient cohorts. We conclude that ProteinSeq is promising for screening large numbers of proteins and samples while the technology can provide a much-needed platform for validation of diagnostic markers in biobank samples and in clinical use

Systemic Inflammation in Preclinical Ulcerative Colitis

Background & Aims: Preclinical ulcerative colitis is poorly defined. We aimed to characterize the preclinical systemic inflammation in ulcerative colitis, using a comprehensive set of proteins. Methods: We obtained plasma samples biobanked from individuals who developed ulcerative colitis later in life (n = 72) and matched healthy controls (n = 140) within a population-based screening cohort. We measured 92 proteins related to inflammation using a proximity extension assay. The biologic relevance of these findings was validated in an inception cohort of patients with ulcerative colitis (n = 101) and healthy controls (n = 50). To examine the influence of genetic and environmental factors on these markers, a cohort of healthy twin siblings of patients with ulcerative colitis (n = 41) and matched healthy controls (n = 37) were explored. Results: Six proteins (MMP10, CXCL9, CCL11, SLAMF1, CXCL11 and MCP-1) were up-regulated (P < .05) in preclinical ulcerative colitis compared with controls based on both univariate and multivariable models. Ingenuity Pathway Analyses identified several potential key regulators, including interleukin-1ß, tumor necrosis factor, interferon-gamma, oncostatin M, nuclear factor-¿B, interleukin-6, and interleukin-4. For validation, we built a multivariable model to predict disease in the inception cohort. The model discriminated treatment-naïve patients with ulcerative colitis from controls with leave-one-out cross-validation (area under the curve = 0.92). Consistently, MMP10, CXCL9, CXCL11, and MCP-1, but not CCL11 and SLAMF1, were significantly up-regulated among the healthy twin siblings, even though their relative abundances seemed higher in incident ulcerative colitis. Conclusions: A set of inflammatory proteins are up-regulated several years before a diagnosis of ulcerative colitis. These proteins were highly predictive of an ulcerative colitis diagnosis, and some seemed to be up-regulated already at exposure to genetic and environmental risk factors. © 2021 The Author

A whole-genome sequence and transcriptome perspective on HER2-positive breast cancers

HER2-positive breast cancer has long proven to be a clinically distinct class of breast cancers for which several targeted therapies are now available. However, resistance to the treatment associated with specific gene expressions or mutations has been observed, revealing the underlying diversity of these cancers. Therefore, understanding the full extent of the HER2-positive disease heterogeneity still remains challenging. Here we carry out an in-depth genomic characterization of 64 HER2-positive breast tumour genomes that exhibit four subgroups, based on the expression data, with distinctive genomic features in terms of somatic mutations, copy-number changes or structural variations. The results suggest that, despite being clinically defined by a specific gene amplification, HER2-positive tumours melt into the whole luminal-basal breast cancer spectrum rather than standing apart. The results also lead to a refined ERBB2 amplicon of 106 kb and show that several cases of amplifications are compatible with a breakage-fusion-bridge mechanism

Melatonin inhibira lipidnu peroksidaciju u jetri štakora uzrokovanu benzenom

We studied the antioxidative role of melatonin against benzene toxicity in rat liver. The inhibition of mitochondrial and microsomal lipid peroxidation differed between 24-hour (single-dose), 15-day, and 30-day treatments. Inhibition of mitochondrial lipid peroxidation was the highest after the single dose of melatonin, whereas highest microsomal inhibition was recorded after 30 days of melatonin treatment. No signifi cant difference was recorded between 15-day and 30-day treatments. Cytochrome P4502E1 (CYP4502E1) activity declined after the single-dose and 15-day melatonin treatment in the benzenetreated group, but it rose again, though not signifi cantly after 30 days of treatment. Liver histopathology generally supported these fi ndings. Phenol concentration in the urine samples declined in melatonin and benzene-treated rats. Our results show that melatonin affects CYP4502E1, which is responsible for benzene metabolism. Inhibition of its metabolism correlated with lower lipid peroxidation. In conclusion, melatonin was found to be protective against lipid peroxidation induced by benzene.Istražena je antioksidacijska uloga melatonina u zaštiti protiv toksičnoga djelovanja benzena u jetri štakora. Utvrđeno je da kratkoročno odnosno dugoročnije liječenje štakora melatoninom u različitoj mjeri štiti štakore istodobno izložene benzenu. Inhibicija lipidne peroksidacije mitohondrija i mikrosoma bila je različita nakon 24 h, 15 dana, odnosno 30 dana liječenja melatoninom. Najveća inhibicija lipidne peroksidacije mitohondrija zamijećena je nakon primjene jednokratne doze melatonina, dok je najizraženija inhibicija u mikrosomima zamijećena nakon 30 dana liječenja melatoninom. Slična istraživanja pokazuju da razina glutationa (GSH) najviše raste nakon 24 h liječenja melatoninom. Nije zamijećena razlika između liječenja u trajanju od 15 odnosno 30 dana. U štakora koji su uz benzen istodobno primali i melatonin razine citokroma P4502E1 pale su nakon 24 h odnosno 15 dana izloženosti. U štakora koji su primali samo melatonin te su razine nakon 30 dana statistički neznačajno porasle u odnosu na skupinu izloženu samo benzenu. Histopatološka analiza jetre načelno je potvrdila ove nalaze. Koncentracije fenola u mokraći bile su niže u štakora koji su istodobno primali melatonin i benzen. Ovi rezultati pokazuju da melatonin utječe na citokrom P4502E1, koji je odgovoran za metabolizam benzena. Inhibira li se njegov metabolizam, smanjuje se lipidna peroksidacija. Zaključak je da melatonin štiti od lipidne peroksidacije uzrokovane benzenom

Intercrops of grass with legumes as green manure for agroecological systems.

The stud article aimed to assess the accumulation and rates of nutrients in the biomass of the consortium of millet and leguminous plants for green fertilisation. The treatments were consortia of millet with four different leguminous plants: Cajanus cajan, Canavalia ensiformis, Mucuna aterrima, and Dolichos lablab. The treatments were distributed in a completely randomised design with four replications. The species of each consortium were planted in a line, at a distance of one metre apart. The aerial part of the plants was harvested after 90 days to determine the botanical composition, intercropping biomass, and the amount and accumulation of macronutrients in the biomass. The Millet mass did not differ among the consortia. However, among the legumes, M. aterrima has the highest mass (2806.31 kg/ha DM), which is reflected in the lower ratio of leguminous grasses in the millet consortium with M. aterrima (4.61). The consortia affected the rate and accumulation of P, B, and Fe. The biomass of the millet consortium with C. cajan presented the lowest rate. In addition, the accumulation of K, Mg, and Zn was low in this consortium. The biomass of millet intercrops with M. aterrima, D. lablab and C. ensiformis showed higher accumulations of K, Ca, and Mg. The highest accumulation of N was observed in the biomass of the consortium with M. aterrima (50.71 kg/ha). The rates and accumulations of Cu and Zn were higher in the consortium with M. aterrima. The consortium of millet with the leguminous plants is a sustainable alternative for fertilisation. The consortia with M. aterrima and D. lablab are the most promising ones, due to the higher proportion of plants

Development of Epitope-Blocking ELISA for Universal Detection of Antibodies to Human H5N1 Influenza Viruses

10.1371/journal.pone.0004566PLoS ONE4