Genetics

We present Raptor, a tool for approximately searching many queries in large collections of nucleotide sequences. In comparison with similar tools like Mantis and COBS, Raptor is 12-144 times faster and uses up to 30 times less memory. Raptor uses winnowing minimizers to define a set of representative k-mers, an extension of the Interleaved Bloom Filters (IBF) as a set membership data structure, and probabilistic thresholding for minimizers. Our approach allows compression and a partitioning of the IBF to enable the effective use of secondary memory.

With over 1,000 nuclear genes that could potentially cause a mitochondrial disorder, the current diagnostic approach requires targeted molecular analysis, guided by a combination of clinical and biochemical features. However, the expanding molecular and clinical spectrum means that this approach does not always yield a result. Here we report the unusual clinical presentation of "Progressive External Ophthalmoplegia (PEO) plus" Leigh syndrome in three children from a consanguineous family where exome sequencing identified mutations in NDUFS8. NDUFS8 is a nuclearencoded structural core protein of complex I, and mutations are expected to cause infantile onset and severe disease. Our patients had a later onset, milder and a clinically distinct phenotype, and this gene would not normally be considered in this context. Being untargeted to specific genes, whole exome analysis has the potential to re-write the phenotype and reveal an unexpected molecular aetiology, as illustrated by this family.

The kiwifruit (Actinidia deliciosa cv. ‘Hayward’), which shows climacteric characteristics, continues to ripen after harvest. In this process, quality losses occur in fruits, and this causes economic losses. The post-harvest storage conditions are essential in preventing these losses. The main purpose of this study was to assess the effect of agro-ecological conditions on quality traits and bioactive compounds of the kiwifruit throughout the shelf life. In this study, kiwifruit grown in 5 different locations (Ordu, Giresun, Rize, Samsun, and Yalova) constituted the plant material of the study. The fruits treated with modified atmosphere packaging (MAP) were stored at 0 ± 0.5 °C and 90 ± 5% relative humidity (RH) for 150 days in cold storage. For shelf life measurements, fruits were kept at 20 ± 1 °C and 65 ± 5% RH for 5 d. Quality analysis was performed at monthly intervals (at harvest, 30th, 60th, 90th, 120th, and 150th d). In this study, the lowest respiration rate at the end of t...

Herein we have engineered a smart nuclear targeting thiol-modified riboflavin-gold nano assembly, RfS@AuNPs, which accumulates selectively in nucleus without any nuclear-targeting peptides (NLS/RGD) and shows photophysically in vitro DNA intercalation. A theoretical model using Molecular Dynamics has been developed to probe the mechanism of formation and stability as well as dynamics of the RfS@AuNPs in aqueous solution and within DNA microenvironment. The RfS@AuNPs facilitate the binucleated cell formation that is reflected in the significant increase of DNA damage marker, γ-H2AX as well as the arrest of most of the HeLa cells at pre-G1 phase indicating cell death. Moreover, a significant upregulation of apoptotic markers confirms that the cell death occurs through apoptotic pathway. Analyses of the microarray gene expression of RfS@AuNPs treated HeLa cells show significant alterations in vital biological processes necessary for cell survival. Taken together, our study reports a un...

Actinobacillus pleuropneumoniae is the etiologic agent of porcine contagious pleuropneumonia, a cause of considerable world wide economic losses in the swine industry. We sequenced the complete genome of A. pleuropneumoniae, JL03, an isolate of serotype 3 prevalent in China. Its genome is a single chromosome of 2,242,062 base pairs containing 2,097 predicted proteincoding sequences, six ribosomal rRNA operons, and 63 tRNA genes. Preliminary analysis of the genomic sequence and the functions of the encoded proteins not only confirmed the present physiological and pathological knowledge but also offered new insights into the metabolic and virulence characteristics of this important pathogen. We identified a full spectrum of genes related to its characteristic chemoheterotrophic catabolism of fermentation and respiration with an incomplete TCA system for anabolism. In addition to confirming the lack of ApxI toxin, identification of a nonsense mutation in apxIVA and a 59-proximal truncation of the flp operon deleting both its promoter and the flp1flp2tadV genes have provided convincing scenarios for the low virulence property of JL03. Comparative genomic analysis using the available sequences of other serotypes, probable strain (serotype)specific genomic islands related to capsular polysaccharides and lipopolysaccharide O-antigen biosyntheses were identified in JL03, which provides a foundation for future research into the mechanisms of serotypic diversity of A. pleuropneumoniae.

The Magnaporthe oryzae avirulence gene AvrPiz-t activates immunity in a gene-for-gene fashion to rice mediated by the blast resistance gene Piz-t. To dissect the molecular mechanism underlying their recognition, we initiated the cloning of AvrPiz-t using a map-based cloning strategy. The AvrPiz-t gene was delimited to an approximately 21-kb genomic fragment, in which six genes were predicted. Complementation tests of each of these six candidate genes led to the final identification of AvrPiz-t, which encodes a 108-amino-acid predicted secreted protein with unknown function and no homologues in M. oryzae or in other sequenced fungi. We found that AvrPiz-t is present in the virulent isolate GUY11 but contains a Pot3 insertion at a position 462 bp upstream from the start codon. Complementation tests of AvrPiz-t genes driven by promoters of varying length revealed that a promoter larger than 462 bp is essential to maintain the AvrPiz-t function. These results suggest that a Pot3 inserti...

Nonalcoholic fatty liver disease (NAFLD) is a global pandemic that affects one-quarter of the world’s population. NAFLD includes a spectrum of progressive liver disease from steatosis to nonalcoholic steatohepatitis (NASH), fibrosis, and cirrhosis and can be complicated by hepatocellular carcinoma. It is strongly associated with metabolic syndromes, obesity, and type 2 diabetes, and it has been shown that metabolic dysregulation is central to its pathogenesis. Recently, it has been suggested that metabolic- (dysfunction) associated fatty liver disease (MAFLD) is a more appropriate term to describe the disease than NAFLD, which puts increased emphasis on the important role of metabolic dysfunction in its pathogenesis. There is strong evidence that mitochondrial dysfunction plays a significant role in the development and progression of NAFLD. Impaired mitochondrial fatty acid oxidation and, more recently, a reduction in mitochondrial quality, have been suggested to play a major role i...

In autosomal dominant polycystic kidney disease (ADPKD), total kidney volume (TKV) is regarded as an important biomarker of disease progression and different methods are available to assess kidney volume. The purpose of this study was to identify the most efficient kidney volume computation method to be used in clinical studies evaluating the effectiveness of treatments on ADPKD progression. We measured single kidney volume (SKV) on two series of MR and CT images from clinical studies on ADPKD (experimental dataset) by two independent operators (expert and beginner), twice, using all of the available methods: polyline manual tracing (reference method), free-hand manual tracing, semi-automatic tracing, Stereology, Mid-slice and Ellipsoid method. Additionally, the expert operator also measured the kidney length. We compared different methods for reproducibility, accuracy, precision, and time required. In addition, we performed a validation study to evaluate the sensitivity of these me...

The composition of the gut microbiome in industrialized populations differs from those living traditional lifestyles. However, it has been difficult to separate the contributions of human genetic and geographic factors from lifestyle. Whether shifts away from the foraging lifestyle that characterize much of humanity's past influence the gut microbiome, and to what degree, remains unclear. Here, we characterize the stool bacterial composition of four Himalayan populations to investigate how the gut community changes in response to shifts in traditional human lifestyles. These groups led seminomadic hunting-gathering lifestyles until transitioning to varying levels of agricultural dependence upon farming. The Tharu began farming 250-300 years ago, the Raute and Raji transitioned 30-40 years ago, and the Chepang retain many aspects of a foraging lifestyle. We assess the contributions of dietary and environmental factors on their gut-associated microbes and find that differences in the lifestyles of Himalayan foragers and farmers are strongly correlated with microbial community variation. Furthermore, the gut microbiomes of all four traditional Himalayan populations are distinct from that of the Americans, indicating that industrialization may further exacerbate differences in the gut community. The Chepang foragers harbor an elevated abundance of taxa associated with foragers around the world. Conversely, the gut microbiomes of the populations that have transitioned to farming are more similar to those of Americans, with agricultural dependence and several associated lifestyle and environmental factors correlating with the extent of microbiome divergence from the foraging population. The gut microbiomes of Raute and Raji reveal an intermediate state between the Chepang and Tharu, indicating that divergence from a stereotypical foraging microbiome can occur within a single generation. Our results also show that environmental factors such as drinking

Introduction: The Y chromosome, transmitted exclusively through the paternal line, is a well-established tool for verifying genealogical data. The Kazakh tribe Zhetiru in Kazakhstan, comprising seven clans, has conflicting historical and genealogical narratives regarding its origin-either as a union of seven independent clans or as descendants of a single common ancestor. A detailed genetic investigation has not yet addressed this question. Methods: 350 male volunteers from the Zhetiru tribe were analyzed using 23 Y-STR loci and 17 Y-SNPs. We calculated genetic distances using Arlequin and STRAF, and explored genetic structure with median-joining networks using a comparative dataset of over 3,000 Kazakh individuals. Results: At the tribal level, haplotype diversity (0.997) and haplogroup diversity (0.91) are high. However, at the clan level, haplotypic diversity decreases, revealing clear founder effects in the main haplogroups of Kerderi (R1a1a), Kereit (N1a2), Tama (C2a1a3), and Teleu (J2a2). The genetic structures of Zhagalbaily, Ramadan, and Tabyn indicate additional sub-clan founders. The ages of key clusters suggest stable genetic lineages for over 1,000 years. Zhetiru clans do not form a distinct genetic cluster among Kazakh tribes but demonstrate genetic affinities with others. Conclusion: This study demonstrates the effective application of genetic genealogy approaches in verifying historical and genealogical records concerning the Zhetiru tribe and determining its origin from distinct, genetically independent clans.

The New Word screwworm, Cochliomyia hominivorax (Coquerel 1858) (Diptera: Calliphoridae), is one of the most important insect pests of livestock in the Neotropical region. In this work, polymerase chain reaction-restriction fragment length polymorphism of mitochondrial DNA (mtDNA) was used to study the diversity and population structure of seven geographically distinct populations of C. hominivorax from most of the important livestock areas in Uruguay. The control region (AϩT/12S) and subunits 1 and 2 of cytochrome oxidase (cox1/cox2) were ampliÞed and digested with restriction endonucleases. Nine haplotypes were observed among the populations sampled. The mean nucleotide diversity and the haplotype diversity indicated high mtDNA variability in this species. The similarity index, average nucleotide divergence, and analysis of molecular variance results showed no evidence of subpopulation differentiation, indicating that the C. hominivorax populations of Uruguay form a single panmitic population. The distribution pattern of the genetic variation in natural populations of C. hominivorax and the implications of these results for establishing control program are discussed.

The 11q terminal deletion disorder (11q-) is a rare chromosomal disorder caused by a deletion in distal 11q. Fifty-six percent of patients have clinically significant congenital heart defects. A cardiac ''critical region'' has been identified in distal 11q that contains over 40 annotated genes. In this study, we identify the distal breakpoint of a patient with a paracentric inversion in distal 11q who had hypoplastic left heart and congenital thrombocytopenia. The distal breakpoint mapped to JAM-3, a gene previously identified as a candidate gene for causing HLHS in 11q-. To determine the role of JAM-3 in cardiac development, we performed a comprehensive cardiac phenotypic assessment in which the mouse homolog for JAM-3, JAM-C, has been deleted. These mice have normal cardiac structure and function, indicating that haplo-insufficiency of JAM-3 is unlikely to cause the congenital heart defects that occur in 11q-patients. Notably, we identified a previously undescribed phenotype, jitteriness, in most of the sick or dying adult JAM-C knockout mice. These data provide further insights into the identification of the putative disease-causing cardiac gene(s) in distal 11q, as well as the functions of JAM-C in normal organ development.

Neurogenetic disorders with distinct genetic etiologies and known psychiatric phenotypes present a compelling model to study the links between genotype and phenotype. In recent years, the study of quantitative endophenotypes has become increasingly relevant in garnering a comprehensive understanding of psychiatric dysfunction. Neurofibromatosis Type 1 (NF1) and 22q11.2 Deletion Syndrome (22q11DS) are two compelling examples of neurogenetic disorders that are highly penetrant for neuropsychiatric phenotypes, and are also characterized by prefrontal cognitive dysfunction. We investigated endophenotypes of executive control in these populations, using a reverse-genetic approach. In Chapter 2, we measured risk-taking behavior using a child-friendly gambling task in patients with NF1 and controls (N=29 NF1, 23 controls). We used functional magnetic resonance imaging (fMRI) to investigate neural activity associated with risky decision making, as well as age-associated changes in these behavioral and neural processes. Behaviorally, patients with NF1 iii tended to made fewer risky decisions than controls. Neuroimaging analyses revealed significant hypoactivation of multiple brain regions involved in higher-order semantic processing and motivation (i.e., anterior cingulate, paracingulate, supramarginal, and angular gyri) in patients with NF1 relative to controls, in both decision-making and outcome phases of the task. We also observed atypical age-associated changes in neural activity in patients with NF1, such that during risk taking, neural activity tended to decrease with age in controls, whereas it tended to increase with age in patients with NF1. Findings suggest that developmental trajectories of neural activity during risky decision-making may be disrupted in youth with NF1. In Chapter 3, we reviewed recent literature on the utility of studying endophenotypes of psychiatric illness in 22q11DS. We provided an overview of neuropsychiatric findings to date, which highlight the value of this syndrome in mapping the developmental trajectory of dimensional phenotypes that traverse multiple diagnostic categories. Potential sources of genetic variability that may contribute to the disorder's heterogeneous presentation were reviewed. We discussed the use of how animal models can readily be developed that recapitulate specific aspects of the syndrome. Future research directions involve translational models and potential for drug screenable targets in the context of this human model system. In Chapter 4, we investigated executive function and its relationship with structural neuroanatomy in patients with 22q11DS and matched controls (N=43 22q11DS, 43 controls), along with cognitive measures that tap behavioral regulation and metacognitive aspects of executive function. Behaviorally, patients with 22q11DS were impaired on multiple executive function measures. Right orbitofrontal cortical thickness showed a differential relationship between real-world executive function in patients with 22q11DS and controls. We also observed a group difference in the relationship between behavioral regulation and metacognition measures iv with thickness of ventral and dorsolateral prefrontal regions, respectively. Findings suggest that executive dysfunction characteristic of 22q11DS is underscored by altered prefrontal cortical structure. In Chapter 5, we investigated gene expression levels and behavioral correlates in patients with 22q11DS and matched controls (N=56 22q11DS, 48 controls). Using real-time quantitative polymerase chain reaction (RT-qPCR), we measured gene expression levels of three genes that are hemizygous in 22q11DS (COMT, DGCR8, and ZDHHC8). We found decreased expression of all three genes in patients with 22q11DS. We found a positive relationship between age and COMT expression in patients with 22q11DS, but not in controls. We also investigated the relationship between gene expression levels and relevant cognitive measures related to executive function, and found interaction effects between group and IQ for DGCR8 and ZDHHC8. Lastly, we found a relationship between working memory and COMT expression in patients with 22q11DS, but not in controls. Results suggest that the relationships between gene expression and cognitive function may differ between patients with 22q11DS and controls. Overall, the collected work provides insight into the use of endophenotypes of executive control in neurogenetic disorders. In clinical psychiatry, current methods for diagnosing psychiatric illness rely on clinical symptoms. Our research is in line with the NIMH RDoC framework, which supports the notion of studying intermediate endophenotypes in order to better diagnose and treat patients with psychiatric illness. Having a comprehensive understanding of the building blocks of psychiatric disease can lead not only to better methods of diagnosis, but also to better treatment strategies. v The dissertation of Rachel Karen Jonas is approved.

Multi‐locus microsatellite typing (MLMT) has been employed to infer the population structure of Phlebotomus papatasi (Scopoli) (Diptera: Psychodidae) sandflies and assign individuals to populations. Phlebotomus papatasi sandflies were collected from 35 sites in 15 countries. A total of 188 P. papatasi individuals were typed using five microsatellite loci, resulting in 113 different genotypes. Unique microsatellite signatures were observed for some of the populations analysed. Comparable results were obtained when the data were analysed with Bayesian model and distance‐based methods. Bayesian statistic‐based analyses split the dataset into two distinct genetic clusters, A and B, with further substructuring within each. Population A consisted of five subpopulations representing large numbers of alleles that were correlated with the geographical origins of the sandflies. Cluster B comprised individuals collected in the Middle East and the northern Mediterranean area. The subpopulations...

Abstrak Kuffea merupakan produk lulur herbal tradisional yang terbuat dari tanaman berkhasiat obat yaitu bubuk daun kelor, bubuk kunyit, dan bubuk kopi. Formulasi lulur bentuk krim yaitu 0,25 ml ekstrak daun kelor, 0,1 ml ekstrak kunyit, 1 ml ekstrak kopi, 1 ml ekstrak kulit kopi, 0,3 gram bubuk kopi, 7 gram tepung beras, 7 gram tepung tapioka, 2 gram butiran scrub, 5 gram asam stearat, 3 gram cetyl alkohol, 0,05 gram propyl paraben, 50 ml aquades, 6 ml propylen glikol, 0,05 gram metyl paraben, dan 0,05 ml parfum. Formulasi lulur bentuk bubuk yaitu 0,5 gram bubuk daun kelor, 0,5 gram bubuk kunyit, 3 gram bubuk kopi, 6 gram bubuk kulit kopi, 16 gram tepung beras, 16 gram tepung tapioka, dan 8 gram butiran scrub. Proses pembuatan produk “Kuffea” yaitu pembuatan butiran scrub, pembuatan ekstrak, dan pembuatan produk jadi lulur. Pengujian produk meliputi uji organoleptik, uji homogenitas, uji pH, dan uji hedonik. Strategi pemasaran produk menggunakan prinsip 4P (Product, Price, Place, P...

Using a method in which DNA adducts are discovered based on their conversion in a nucleotide form to phosphorimidazolides with isotopologue benzoylhistamines (or pbromobenzoylhistamine) prior to detection by MALDI-TOF-MS, we have profiled the adducts that form when calf thymus DNA is reacted in vitro with p-benzoquinone (BQ). We find, as relative values normalized to 100% of adducts observed, 79% BQ-dCMP, 21% BQ-methyl-dCMP (a new DNA adduct), and trace amounts of BQ-dAMP and BQ-dGMP. Since mC is 5% of C in this DNA, the reaction of BQ with DNA in vitro is about five times faster at methyl-C than C. When equal amounts of dCMP and methyl-dCMP are reacted with BQ, equal amounts of the corresponding adducts are observed. Thus, the microenvironment of methyl-C in DNA enhances its reactivity relative to C with BQ. In a prior, similar study, but based on analysis by 32 Ppostlabeling, the second most abundant adduct was assigned to BQ-A, apparently because of comigration of the BQ-A and BQ-methyl-C adducts (as bisphosphates) in the chromatographic step. Since the calf thymus DNA (used as received) was contaminated with RNA, we also detected the ribonucleotide adduct, BQ-CMP.

The mechanism of (CAG)n repeat generation, and related expandable repeat diseases in non-dividing cells, is currently understood in terms of a DNA template-based DNA repair synthesis process involving hairpin stabilized slippage, local error-prone repair via MutSβ (MSH2-MSH3) hairpin protective stabilization, then nascent strand extension by DNA polymerases-β and -δ. We advance a very similar slipped hairpin-stabilized model involving MSH2-MSH3 with two key differences: the copying template may also be the nascent pre-mRNA with the repair pathway being mediated by the Y-family error-prone enzymes DNA polymerase-η and DNA polymerase-κ acting as reverse transcriptases. We argue that both DNA-based and RNA-based mechanisms could well be activated in affected non-dividing brain cells in vivo. Here, we compare the advantages of the RNA/RT-based model proposed by us as an adjunct to previously proposed models. In brief, our model depends upon dysregulated innate and adaptive immunity cascades involving AID/APOBEC and ADAR deaminases that are known to be involved in normal locus-specific immunoglobulin somatic hypermutation, cancer progression and somatic mutations at many off-target non-immunoglobulin sites across the genome: we explain how these processes could also play an active role in repeat expansion diseases at RNA polymerase II-transcribed genes.

According to the proponents of Developmental Systems Theory and the Causal Parity Thesis, the privileging of the genome as "first among equals" with respect to the development of phenotypic traits is more a reflection of our own heuristic prejudice than of ontology -the underlying causal structures responsible for that specified development no more single out the genome as primary than they do other broadly "environmental" factors. Parting with the methodology of the popular responses to the Thesis, this paper offers a novel criterion for "causal primacy", one that is grounded in the ontology of the unique causal role of dispositional properties. This paper argues that, if the genome is conceptualised as realising dispositional properties that are "directed toward" phenotypic traits, the parity of "causal roles" between genetic and extra-genetic factors is no longer apparent, and further, that the causal primacy of the genome is both plausible and defensible.

The BEEHIVE (Bridging the Evolution and Epidemiology of HIV in Europe) project aims to analyse nearlycomplete viral genomes from >3000 HIV-1 infected Europeans using high-throughput deep sequencing techniques to investigate the virus genetic contribution to virulence. Following the development of a computational pipeline, including a new de novo assembler for RNA virus genomes, to generate larger contiguous sequences (contigs) from the abundance of short sequence reads that characterise the data, another area that determines genome sequencing success is the quality and quantity of the input RNA. A pilot experiment with 125 patient plasma samples was performed to investigate the optimal method for isolation of HIV-1 viral RNA for long amplicon genome sequencing. Manual isolation with the QIAamp Viral RNA Mini Kit (Qiagen) was superior over robotically extracted RNA using either the QIAcube robotic system, the mSample Preparation Systems RNA kit with automated extraction by the m2000sp system (Abbott Molecular), or the MagNA Pure 96 System in combination with the MagNA Pure 96 Instrument (Roche Diagnostics). We scored amplification of a set of four HIV-1 amplicons of ∼1.9, 3.6, 3.0 and 3.5 kb, and subsequent recovery of near-complete viral genomes. Subsequently, 616 BEEHIVE patient samples were analysed to determine factors that influence successful amplification of the genome in four overlapping amplicons using the QIAamp Viral RNA Kit for viral RNA isolation. Both low plasma viral load and high sample age (stored before 1999) negatively influenced the amplification of viral amplicons >3 kb. A plasma viral load of >100,000 copies/ml resulted in successful amplification of all four amplicons for 86% of the samples, this value dropped to only 46% for samples with viral loads of <20,000 copies/ml.

Rift Valley fever virus (RVFV), a Phlebovirus with a genome consisting of three single-stranded RNA segments, is spread by infected mosquitoes and causes large viral outbreaks in Africa. RVFV encodes a nucleoprotein (N) that encapsidates the viral RNA. The N protein is the major component of the ribonucleoprotein complex and is also required for genomic RNA replication and transcription by the viral polymerase. Here we present the 1.6 A ˚crystal structure of the RVFV N protein in hexameric form. The ring-shaped hexamers form a functional RNA binding site, as assessed by mutagenesis experiments. Electron microscopy (EM) demonstrates that N in complex with RNA also forms rings in solution, and a single-particle EM reconstruction of a hexameric N-RNA complex is consistent with the crystallographic N hexamers. The ring-like organization of the hexamers in the crystal is stabilized by circular interactions of the N terminus of RVFV N, which forms an extended arm that binds to a hydrophobic pocket in the core domain of an adjacent subunit. The conformation of the N-terminal arm differs from that seen in a previous crystal structure of RVFV, in which it was bound to the hydrophobic pocket in its own core domain. The switch from an intra-to an inter-molecular interaction mode of the N-terminal arm may be a general principle that underlies multimerization and RNA encapsidation by N proteins from Bunyaviridae. Furthermore, slight structural adjustments of the N-terminal arm would allow RVFV N to form smaller or larger ring-shaped oligomers and potentially even a multimer with a super-helical subunit arrangement. Thus, the interaction mode between subunits seen in the crystal structure would allow the formation of filamentous ribonucleocapsids in vivo. Both the RNA binding cleft and the multimerization site of the N protein are promising targets for the development of antiviral drugs.

RNA sequencing (RNA-seq) is the conventional genome-scale approach used to capture the expression levels of all detectable genes in a biological sample. This is now regularly used in the clinical diagnostic space for cancer patients. While the information gained is intended to impact treatment decisions, numerous technical and quality issues remain. This includes inaccuracies in the dissemination of gene-gene relationships. For such reasons, clinical decisions are still mostly driven by DNA biomarkers, such as gene mutations or fusions. In this study, we aimed to correct for systemic bias based on RNA-sequencing platforms in order to improve our understanding of the gene-gene relationships. To do so, we examined standard pre-processed RNA-seq datasets obtained from three studies conducted by two consortium efforts including The Cancer Genome Atlas (TCGA) and Stand Up 2 Cancer (SU2C). We particularly examined the TCGA Bladder Cancer (n = 408) and Prostate Cancer (n = 498) studies as ...

Background: Acute lymphoblastic leukaemia (ALL) is the most common malignancy in childhood. Despite numerous investigations very little is still known about its aetiology. However, in one genome wide association study conducted to identify the possible genetic risk factors, two allelic variations rs10821936 and rs10994982 in the 3rd intron of the ARID5B gene were identified as possible ALL risk alleles. Association between ARID5B gene variants and ALL risk was also been confirmed for different ethnic groups. Materials and Methods: Eight genetic variants in the gene ARID5B were genotyped - rs10994982, rs7908445, rs7923074, rs10821936, rs10821937, rs7896246, rs10821938 and rs7089424 in 77 ALL patients in remission and in 122 age and gender matched controls; parental samples were also genotyped in 50 cases. Results: Six out of the eight (rs7908445, rs7923074, rs10821936, rs10821937, rs7896246 and rs7089424) analysed allelic variations were identified in the case-control analysis as sta...

BackgroundOrganophosphate (OP) pesticides have been associated with a decline in semen quality, although there are still considerable arguments about the magnitude of the association.ObjectiveThis study provides a systematic review and meta-analysis of the impacts of OP pesticides on semen quality and male reproductive hormones.MethodsThis study was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) protocols. Strategic search was conducted using combined text words as search terms. The eligibility criteria were developed based on Population, Exposure, Comparator, Outcome, and Study designs (PECOS) framework. Relevant data were extracted, risk of bias was evaluated by The Office of Health Assessment and Translation (OHAT) tool, and certainty of evidence was assessed by the Grading of Recommendations Assessment, Development and Evaluation (GRADE) Working Group guidelines. Quantitative meta-analysis was performed by using Review Mana...

Progeria (also known as &quot;Hutchinson-Gilford progeria syndrome&quot;(HGPS) is an extremely rare, severe, genetic condition wherein symptoms resembling aspects of aging are manifested at an early age. The basic objective of this study is how is it responsible for faster ageing than normal? The study of its bioinformatics aspect explaining where the mutation occurs in normal LMNA gene to form mutated Progerin. We explain its sequential and structural aspects in domain and motif. Structural visualization by Marker view software provides the linear structure of LMNA and mutated LMNA. We studied the properties and specificity of Lonafarnib (an edible drug available in market) against Progerin with Docking. Cardiovascular disorders are the major symptoms occurred in Progerin patients. Therefore we found 32 natural compounds with their sources having anti cardiovascular disorders activity. We checked its docking properties and ADMET properties. From this we came to conclude 11 most eff...

The presence of inherited VH region allotypic specificities, a I, a2 or a3, on nearly all rabbit immunoglobulins has presented a paradox. We know the germline contains hundreds of VH genes, and if we assume that most of these are used in the generation of antibody diversity, then we must ask how have the a allotype-encoding regions been maintained over time? On the other hand, if we assume that only one (or a small number) of these VH gene(s) is (are) used in VDJ gene rearrangements, then, how is antibody diversity generated? To address these questions, we have cloned and determined the nucleotide sequence of the 3'-most germline VH genes from the ai, a2 and a3 chromosomes and shown in each case that the 3'-most H gene, VH1-al. VH1-a2. or VH1-a3, encodes an ai, a2 or a3 VH region, respectively. Analysis of rearranged VDJ genes from leukemic B cells showed that VHl was utilized in these rearrangements. Based on these data, we propose that the allelic inheritance of the VH allotypes is explained by the preferential usage of the VHI gene in VDJ rearrangements. Support for this hypothesis was obtained from analysis of the mutant rabbit Alicia in which most serum Ig molecules do not have VHa allotypic specificities, but instead have so-called VHa-negative Ig molecules. In this rabbit, V H 1 is not expressed as it has been deleted. Analysis of cDNA clones from spleen of Alicia rabbits suggests that the expressed VHanegative molecules also are encoded by a single germline VH gene. Thus, we suggest that nearly all rabbit VH regions are encoded by one to two germline VH genes and that antibody diversity is generated primarily by somatic hypermutation and gene conversion.

Background: Neuroinflammation is a hallmark of neurodegenerative disease and a significant component of the pathology of Alzheimer's disease (AD). Patients present with extensive microgliosis along with elevated proinflammatory signaling in the central nervous system and periphery. However, the role of peripheral myeloid cells in mediating and influencing AD pathogenesis remains unresolved. Methods: Peripheral myeloid cells were isolated from peripheral blood of patients with prodromal AD (n = 44), mild AD dementia (n = 25), moderate/severe AD dementia (n = 28), and age-matched controls (n = 54). Patients were evaluated in the clinic for AD severity and categorized using Clinical Dementia Rating (CDR) scale resulting in separation of patients into prodromal AD (CDR0.5) and advancing forms of AD dementia (mild-CDR1 and moderate/severe-CDR2/3). Separation of peripheral myeloid cells into mature monocytes or immature MDSCs permitted the delineation of population changes from flow cytometric analysis, RNA phenotype analysis, and functional studies using T cell suppression assays and monocyte suppression assays. Results: During stages of AD dementia (CDR1 and 2/3) peripheral myeloid cells increase their pro-inflammatory gene expression while at early stages of disease (prodromal AD-CDR0.5) pro-inflammatory gene expression is decreased. MDSCs are increased in prodromal AD compared with controls (16.81% vs 9.53%) and have markedly increased suppressive functions: 42.4% suppression of activated monocyte-produced IL-6 and 78.16% suppression of T cell proliferation. In AD dementia, MDSC populations are reduced with decreased suppression of monocyte IL-6 (5.22%) and T cell proliferation (37.61%); the reduced suppression coincides with increased pro-inflammatory signaling in AD dementia monocytes. Conclusions: Peripheral monocyte gene expression is pro-inflammatory throughout the course of AD, except at the earliest, prodromal stages when pro-inflammatory gene expression is suppressed. This monocyte biphasic response is associated with increased numbers and suppressive functions of MDSCs during the early stages and decreased numbers and suppressive functions in later stages of disease. Prolonging the early protective suppression and reversing the later loss of suppressive activity may offer a novel therapeutic strategy.

Background: Neuroinflammation is a hallmark of neurodegenerative disease and a significant component of the pathology of Alzheimer's disease (AD). Patients present with extensive microgliosis along with elevated proinflammatory signaling in the central nervous system and periphery. However, the role of peripheral myeloid cells in mediating and influencing AD pathogenesis remains unresolved. Methods: Peripheral myeloid cells were isolated from peripheral blood of patients with prodromal AD (n = 44), mild AD dementia (n = 25), moderate/severe AD dementia (n = 28), and age-matched controls (n = 54). Patients were evaluated in the clinic for AD severity and categorized using Clinical Dementia Rating (CDR) scale resulting in separation of patients into prodromal AD (CDR0.5) and advancing forms of AD dementia (mild-CDR1 and moderate/severe-CDR2/3). Separation of peripheral myeloid cells into mature monocytes or immature MDSCs permitted the delineation of population changes from flow cytometric analysis, RNA phenotype analysis, and functional studies using T cell suppression assays and monocyte suppression assays. Results: During stages of AD dementia (CDR1 and 2/3) peripheral myeloid cells increase their pro-inflammatory gene expression while at early stages of disease (prodromal AD-CDR0.5) pro-inflammatory gene expression is decreased. MDSCs are increased in prodromal AD compared with controls (16.81% vs 9.53%) and have markedly increased suppressive functions: 42.4% suppression of activated monocyte-produced IL-6 and 78.16% suppression of T cell proliferation. In AD dementia, MDSC populations are reduced with decreased suppression of monocyte IL-6 (5.22%) and T cell proliferation (37.61%); the reduced suppression coincides with increased pro-inflammatory signaling in AD dementia monocytes. Conclusions: Peripheral monocyte gene expression is pro-inflammatory throughout the course of AD, except at the earliest, prodromal stages when pro-inflammatory gene expression is suppressed. This monocyte biphasic response is associated with increased numbers and suppressive functions of MDSCs during the early stages and decreased numbers and suppressive functions in later stages of disease. Prolonging the early protective suppression and reversing the later loss of suppressive activity may offer a novel therapeutic strategy.

Priapism is a disorder in which prolonged penile erection persists uncontrollably, potentially leading to tissue damage. Priapism commonly afflicts patient populations with severely low nitric oxide (NO) bioavailability. As NO is a primary mediator of erection, the molecular mechanisms involved in priapism pathophysiology associated with low NO bioavailability are not well understood. The objective of this study was to identify dysregulated molecular targets and signaling pathways in penile tissue of a mouse model of low NO bioavailability that have potential relevance to priapism. Neuronal + endothelial NO synthase double knockout mice (NOS1/3 -/-) were used as a model of low NO bioavailability. Priapic-like activity was demonstrated in the NOS1/3 -/-mice relative to wild type (WT) mice by measurement of prolonged erections following cessation of electrical stimulation of the cavernous nerve. Penile tissue was processed and analyzed by reversed-phase liquid chromatography tandem mass spectrometry. 1279 total proteins were identified and quantified by spectral counting, 46 of which were downregulated and 110 of which were upregulated in NOS1/3 -/-vs. WT (P<0.05). Ingenuity Pathway Analysis of differentially expressed proteins revealed increased protein kinase A and G-protein coupled receptor signaling in NOS1/3 -/-penis which represent potential mechanisms contributing to priapism secondary to low NO bioavailability.

Catheter-associated urinary tract infection (CAUTI) is defined as a urinary tract infection associated with catheter placement for more than two consecutive days. Hence, antibiotic resistance in the context of CAUTIs represents a substantial challenge. The aim of this study was to present the characteristics of patients with CAUTI and the susceptibility pattern of CAUTI bacteria in the national reference hospital of the Sumatra region of Indonesia. A cross-sectional study was conducted at H. Adam Malik General Hospital, Medan, Indonesia, from 2020 to 2021, using a total sampling. All CAUTI patients included were on catheterization and diagnosed based on the Centers for Disease Control and Prevention (CDC) guidelines. The patient's urine culture and antibiotic susceptibility test were carried out on the patient's admitted urine sample for further assessment. Identification of bacteria, antibiotic susceptibility test, and the extended-spectrum betalactamase (ESBL) test for Escherichia coli and Klebsiella pneumoniae were conducted using the VITEK-2 Compact. A total of 74 CAUTI patients were included in the study, 59.5% were female, 54.1% were 46-65 years old, and a third had cardiovascular disease comorbidities (33.8%). A total of 83 CAUTI-associated bacteria were isolated. The majority were Gram-negative bacteria (74.7%), and the most bacteria isolated was E. coli (31.3%), followed by K. pneumoniae, Enterococcus faecalis, Acinetobacter baumannii, and Enterococcus faecium. The ESBL test was positive mostly in K. pneumoniae (100%) and E. coli (76.9%). CAUTI-associated E. coli was susceptible to tigecycline, meropenem, ertapenem, nitrofurantoin, and gentamicin. The isolated K. pneumoniae was susceptible to tigecycline, meropenem, ertapenem, and amikacin. While E. faecalis showed susceptibility to tigecycline, nitrofurantoin, vancomycin, imipenem, linezolid, ampicillin, piperacillin/tazobactam, amoxicillin/clavulanic acid, ampicillin/sulbactam, and piperacillin.

Understanding plant stress memory under extreme temperatures such as cold and heat could contribute to plant development. Plants employ different types of stress memories, such as somatic, intergenerational and transgenerational, regulated by epigenetic changes such as DNA and histone modifications and microRNAs (miRNA), playing a key role in gene regulation from early development to maturity. In most cases, cold and heat stresses result in short-term epigenetic modifications that can return to baseline modification levels after stress cessation. Nevertheless, some of the modifications may be stable and passed on as stress memory, potentially allowing them to be inherited across generations, whereas some of the modifications are reactivated during sexual reproduction or embryogenesis. Several stress-related genes are involved in stress memory inheritance by turning on and off transcription profiles and epigenetic changes. Vernalization is the best example of somatic stress memory. C...

The knowledge of the extent and pattern of diversity in the crop species is a prerequisite for any crop improvement as it helps breeders in deciding suitable breeding strategies for their future improvement. Rice is the main staple crop in India with the large number of varieties released every year. Studies based on the small set of rice genotypes have reported a loss in genetic diversity especially after green revolution. However, a detailed study of the trend of diversity in Indian rice varieties is lacking. SSR markers have proven to be a marker of choice for studying the genetic diversity. Therefore, the present study was undertaken with the aim to characterize and assess trends of genetic diversity in a large set of Indian rice varieties (released between 1940-2013), conserved in the National Gene Bank of India using SSR markers. A set of 729 Indian rice varieties were genotyped using 36 HvSSR markers to assess the genetic diversity and genetic relationship. A total of 112 all...

Step 1: To a sealed tube were added 5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyridin-2amine SI-1 (2.2 g, 10 mmol), 2-iodopyrazine SI-2 (2.06 g, 10 mmol), Pd(PPh 3 ) 4 (577 mg, 0.5 mmol), toluene (70 mL), ethanol (15 mL) and 2M Na 2 CO 3 (15 mL). The reaction mixture was bubbled with nitrogen for 2 minutes and stirred at 90 °C for 10 hours. After cooled down to room temperature, the solvents were evaporated and the residue was redissovled in dichloromethane (200 ml), treated with 1M HCl aqueous solution (50 mL). The two layers were separated and the aqueous layer was treated with 10% NaOH aqueous solution to adjust the pH to around 13. The

It is still a matter of debate if nature provides conditions for abiogenic production of hydrocarbons. Methane (C1) and the C2+ alkanes emanating from ultramafic hydrothermal systems such as Lost City have been considered to be abiogenic in origin, mainly because of the occurrence of an isotopic reversal between methane and the C2+hydrocarbons and C1/C2+ ratios >1000 [1]. Abiogenic production of methane has been postulated to occur under the relatively oxidizing redox conditions of continental-hydrothermal systems, too. It was observed that temperatures received from the H 2 -H 2 O-CO-CO 2 -CH 4 geoindicator were coincident with temperatures derived from carbon isotope partitioning between CO 2 and CH 4 in gases released from the Mediterranean volcanic-hydrothermal systems of Nisyros (Greece), Vesuvio and Ischia (both Italy) . Such equilibrium pattern, if not fortuitous, can only be obtained if mantle-and marine limestone-derived CO 2 is reduced to CH 4 . At Nisyros, observed C1/C2+ ratios from 300-4000 are in agreement with an abiogenic origin of the methane. Ethane and propane, however, were shown to be non-genetic with CO 2 and methane. C1/C2 and C2/C3 distribution ratios may point to the admixture of small amounts of hydrocarbons deriving from the thermal decomposition of organic matter along with abiogenically equilibrated methane essentially devoid of the higher hydrocarbons . Here, we provide new isotopic and hydrocarbon concentration data on several Mediterranean volcanichydrothermal systems, including Nisyros, Vesuvio, Ischia, Vulcano, Solfatara and Pantelleria. Wherever possible, we have extended our data set for the hydrogen isotope composition of CH 4 and H 2 , n-alkane-and alkene/alkanedistribution ratios. At Nisyros, measured alkene/alkane-and H 2 /H 2 O concentration ratios confirm the attainment of equilibrium between CO 2 and CH 4 . CO 2 and CH 4 appear to have equilibrated in the liquid phase at temperatures of ∼360˚C and redox conditions closely corresponding to the metastable mineral paragenesis of fayalitehematite-quartz. At Pantelleria and Solfatara, apparent isotopic CH 4 -CO 2 equilibration temperatures of ∼560˚C and ∼450˚C, respectively, are in agreement with measured alkene/alkane-and H 2 /H 2 O ratios, too. However, at Baia di Levante (Vulcano), these concentration ratios do not correspond to the apparent carbon isotopic temperature. These findings imply that carbon isotopic analysis of discharged CO 2 and CH 4 might be a powerful tool to determine temperatures of volcanic aquifers. Alkene/alkane and H 2 /H 2 O concentration ratios should be measured along with the carbon isotopic composition of CO 2 and CH 4 to be able to check independently if isotopic equilibrium between CO 2 and CH 4 has been attained.

Objectives: This study aimed to systematically identify and evaluate the readability and document complexity of currently available family history tools for the general public. Methods: Three steps were undertaken to identify family history tools for evaluation: (a) Internet searches, (b) expert consultation, and (c) literature searches. Tools identified were assessed for readability using the Simple Measure of Gobbledygook (SMOG) readability formula. The complexity of documents (i.e., forms collecting family history information) was assessed using the PMOSE/IKIRSCH document readability formula. Results: A total of 78 tools were identified, 47 of which met the criteria for inclusion. SMOG reading grade levels for multimedia-based tools ranged from 10.1 to 18.3, with an average score of 13.6. For print-based tools, SMOG ranged from 8.7 to 14.1, with an average score of 12.0. Document complexity ranged from very low complexity (level 1 proficiency) to high complexity (level 4 proficie...

Using a combination of homozygosity mapping and whole‐exome sequencing (WES), we identified a novel missense c.1819G&gt;A mutation (G607S) in the endothelin‐converting enzyme‐like 1 (ECEL1) gene in a consanguineous pedigree of Turkish origin presenting with a syndrome of camptodactyly, scoliosis, limited knee flexion, significant refractive errors and ophthalmoplegia. ECEL1 mutations were recently reported to cause recessive forms of distal arthrogryposis. This report expands on the molecular basis and the phenotypic spectrum of ECEL1‐associated congenital contracture syndromes.

Duane syndrome is a congenital eye movement disorder characterized most typically by absence of abduction, restricted adduction, and retraction of the globe on attempted adduction. Duane syndrome can be coinherited with radial ray anomalies as an autosomal dominant trait, referred to as "Okihiro syndrome" or "Duane radial ray syndrome" (DRRS). We ascertained three pedigrees with DRRS and mapped their disease gene to a 21.6-cM region of chromosome 20 flanked by markers D20S888 and D20S102. A new member of the SAL family of proposed C 2 H 2 zinc finger transcription factors, SALL4, falls within the region. Mutation analysis of SALL4 in the three pedigrees revealed one nonsense and two frameshift heterozygous mutations. SALL4 represents the first identified Duane syndrome gene and the second malformation syndrome resulting from mutations in SAL genes and likely plays a critical role in abducens motoneuron development. Several forms of congenital ophthalmoplegia are hypothesized to result from errors in the development of the ocular cranial nuclei . The most common of these, Duane syndrome (MIM 126800 and MIM 604356), is characterized by restricted or absent abduction and variably restricted adduction with retraction of the globe on attempted adduction, and results from absence of the abducens (nVI) motoneurons and nerve, with sparing of the internuclear neurons . Two Duane syndrome loci (DURS1 and DURS2) have been mapped, but neither gene has been identified . Duane syndrome can be coinherited with radial anomalies in an autosomal dominant fashion (fig. ). In affected individuals, radial dysplasia ranges from hypoplasia of the thenar eminence to absence of the radial bone or forearm. Variable expression of sensorineural hearing loss and cardiac, renal, vertebral, and lower extremity malformations can occur. De-

Congenital fibrosis of the extraocular muscles type 1 (CFEOM1; OMIM #135700) is an autosomal dominant strabismus disorder associated with defects of the oculomotor nerve. We show that individuals with CFEOM1 harbor heterozygous missense mutations in a kinesin motor protein encoded by KIF21A. We identified six different mutations in 44 of 45 probands. The primary mutational hotspots are in the stalk domain, highlighting an important new role for KIF21A and its stalk in the formation of the oculomotor axis.

The Schizosaccharomycespombe centromere- linked genes, LYS] and CYHI on chromosome I and TPS13 and RAN) on chromosome II, have been isolated. The genetic order of these markers with respect to their centromeres was deter- mined to establish relative directionality on the genetic and physical maps. Chromosome walking toward the centromeres reveals a group of repetitive sequences that occur only in the centromere regions of chromosomes I and II and at one other specific location in the S. pombe genome, presumably the centromere of chromosome ITH. The major class of large repeated sequence elements is 6.4 kilobases (kb) long (repeat K), portions ofwhich occur at least twice on chromosome II and in several tandemly arranged intact copies at another centromeric location. Repeat K in turn contains groups of smaller repeats. Genetic recombination is strongly suppressed in the centromere II region, which contains at least 30 kb of repeated sequences. Centromeric DNA organization is much more complex in fission yeast than has been described in budding yeast (Saccharomyces cerevisiae), possibly because of the larger more condensed nature of the S. pombe chromosomes.

Centromeric DNA in the fission yeast Schizosaccharomyces pombe was isolated by chromosome walking and by field inversion gel electrophoretic fractionation of large genomic DNA restriction fragments. The centromere regions of the three chromosomes were contained on three SalI fragments (120 kilobases [kb], chromosome III; 90 kb, chromosome II; and 50 kb, chromosome I). Each fragment contained several repetitive DNA sequences, including repeat K (6.4 kb), repeat L (6.0 kb), and repeat B, that occurred only in the three centromere regions. On chromosome II, these repeats were organized into a 35-kb inverted repeat that included one copy of K and L in each arm of the repeat. Site-directed integration of a plasmid containing the yeast LEU2 gene into K repeats at each of the centromeres or integration of an intact K repeat into a chromosome arm had no effect on mitotic or meiotic centromere function. The centromeric repeat sequences were not transcribed and possessed many of the propertie...

The Hemophilus influenzae Hind11 endonuclease cleaves polyoma DNA into two fragments, approximately 90 and 10% the size of polyoma linear DNA. One of the Hind11 sites is located in the H. parainfluenzae HpaII-F fragment, and the other in the HpaII-A fragment. Both sites have the sequence 1 (5,) GTCGAC. CAGCTG 277

Differences in the cervicovaginal microbiota are associated with spontaneous preterm birth (sPTB), a significant cause of infant morbidity and mortality. Although establishing a direct causal link between cervicovaginal microbiota and sPTB remains challenging, recent advancements in sequencing technologies have facilitated the identification of microbial markers potentially linked to sPTB. Despite variations in findings, a recurring observation suggests that sPTB is associated with a more diverse and less stable vaginal microbiota across pregnancy trimesters. It is hypothesized that sPTB risk is likely to be modified via an intricate host-microbe interactions rather than due to the presence of a single microbial taxon or broad community state. Nonetheless, lactobacilli dominance is generally associated with term outcomes and contributes to a healthy vaginal environment through the production of lactic acid/ maintenance of a low pH that excludes other pathogenic microorganisms. Additionally, the innate immunity of the host and metabolic interactions between cervicovaginal microbiota, such as the production of bacteriocins and the use of proteolytic enzymes, exerts a profound influence on microbial populations, activities, and host immune responses. These interplays collectively impact pregnancy outcomes. This review aims to summarize the complexity of cervicovaginal environment and microbiota dynamics, and associations with bacterial vaginosis and sPTB. There is also consideration on how probiotics may mitigate the risk of sPTB and bacterial vaginosis.

Lichen planus (LP) is a relatively common disorder of the stratified squamous epithelia, which is, in many ways, an enigma. This paper is the consensus outcome of a workshop held in Switzerland in 1995, involving a selection of clinicians and scientists with an interest in the condition and its management. The oral (OLP) eruptions usually have a distinct clinical morphology and characteristic distribution, but OLP may also present a confusing array of patterns and forms, and other disorders may clinically simulate OLP. Lesions may affect other mucosae and/or skin. Lichen planus is probably of multifactorial origin, sometimes induced by drugs or dental materials, often idiopathic, and with an immunopathogenesis involving T-cells in particular. The etiopathogenesis appears to be complex, with interactions between and among genetic, environmental, and lifestyle factors, but much has now been clarified about the mechanisms involved, and interesting new associations, such as with liver d...

Transient influx of Ca 2 ϩ constitutes an early element of signaling cascades triggering pathogen defense responses in plant cells. Treatment with the Phytophthora sojae -derived oligopeptide elicitor, Pep-13, of parsley cells stably expressing apoaequorin revealed a rapid increase in cytoplasmic free calcium ([Ca 2 ϩ ] cyt ), which peaked at ‫ف‬ 1 M and subsequently declined to sustained values of 300 nM. Activation of this biphasic [Ca 2 ϩ ] cyt signature was achieved by elicitor concentrations sufficient to stimulate Ca 2 ϩ influx across the plasma membrane, oxidative burst, and phytoalexin production. Sustained concentrations of [Ca 2 ϩ ] cyt but not the rapidly induced [Ca 2 ϩ ] cyt transient peak are required for activation of defense-associated responses. Modulation by pharmacological effectors of Ca 2 ϩ influx across the plasma membrane or of Ca 2 ϩ release from internal stores suggests that the elicitor-induced sustained increase of [Ca 2 ϩ ] cyt predominantly results from the influx of extracellular Ca 2 ϩ . Identical structural features of Pep-13 were found to be essential for receptor binding, increases in [Ca 2 ϩ ] cyt , and activation of defense-associated responses. Thus, a receptormediated increase in [Ca 2 ϩ ] cyt is causally involved in signaling the activation of pathogen defense in parsley.

Background Microsatellites are important markers for livestock including ducks. The development of microsatellites is expensive and labor-intensive. Meanwhile, the in silico approach for mining for microsatellites became a practicable alternative. Therefore, the current study aimed at comparing whole-genome and chromosome-wise microsatellite mining approaches in Muscovy and Mallard ducks and testing the transferability of markers between them. The GMATA software was used for the in silico study, and validation was performed using 26 primers. Results The total number of the detected microsatellites using chromosome-wise was 250,053 and 226,417 loci compared to 260,059 and 238,462 loci using whole genome in Mallards and Muscovies. The frequencies of different motifs had similar patterns using the two approaches. Dinucleotide motifs were predominant (&gt; 50%) in both Mallards and Muscovies. The amplification of the genomes revealed an average number of alleles of 5.08 and 4.96 in Mall...

Background Leber's hereditary optic neuropathy (LHON) is a mitochondrial disorder characterised by complex I defect leading to sudden degeneration of retinal ganglion cells. Although typically associated with pathogenic variants in mitochondrial DNA, LHON was recently described in patients carrying biallelic variants in nuclear genes DNAJC30, NDUFS2 and MCAT. MCAT is part of mitochondrial fatty acid synthesis (mtFAS), as also MECR, the mitochondrial trans-2-enoyl-CoA reductase. MECR mutations lead to a recessive childhood-onset syndromic disorder with dystonia, optic atrophy and basal ganglia abnormalities. Methods We studied through whole exome sequencing two sisters affected by sudden and painless visual loss at young age, with partial recovery and persistent central scotoma. We modelled the candidate variant in yeast and studied mitochondrial dysfunction in yeast and fibroblasts. We tested protein lipoylation and cell response to oxidative stress in yeast. Results Both sisters carried a homozygous pathogenic variant in MECR (p.Arg258Trp). In yeast, the MECR-R258W mutant showed an impaired oxidative growth, 30% reduction in oxygen consumption rate and 80% decrease in protein levels, pointing to structure destabilisation. Fibroblasts confirmed the reduced amount of MECR protein, but failed to reproduce the OXPHOS defect. Respiratory complexes assembly was normal. Finally, the yeast mutant lacked lipoylation of key metabolic enzymes and was more sensitive to H 2 O 2 treatment. Lipoic Acid supplementation partially rescued the growth defect. Conclusion We report the first family with homozygous MECR variant causing an LHON-like optic neuropathy, which pairs the recent MCAT findings, reinforcing the impairment of mtFAS as novel pathogenic mechanism in LHON. ⇒ Further investigations are necessary to well characterise the novel link between mtFAS and LHON. However, MECR should be added to the molecular diagnostic pathway for LHON.

ObjectiveDominant optic atrophy (DOA) is the most common inherited optic neuropathy, with a prevalence of 1:12,000 to 1:25,000. OPA1 mutations are found in 70% of DOA patients, with a significant number remaining undiagnosed.MethodsWe screened 286 index cases presenting optic atrophy, negative for OPA1 mutations, by targeted next generation sequencing or whole exome sequencing. Pathogenicity and molecular mechanisms of the identified variants were studied in yeast and patient‐derived fibroblasts.ResultsTwelve cases (4%) were found to carry novel variants in AFG3L2, a gene that has been associated with autosomal dominant spinocerebellar ataxia 28 (SCA28). Half of cases were familial with a dominant inheritance, whereas the others were sporadic, including de novo mutations. Biallelic mutations were found in 3 probands with severe syndromic optic neuropathy, acting as recessive or phenotype‐modifier variants. All the DOA‐associated AFG3L2 mutations were clustered in the ATPase domain, ...

To evaluate longitudinal retinal ganglion cell inner plexiform layer (GC-IPL) and macular retinal nerve fibre layer (mRNFL) thickness changes in acute Leber&#39;s hereditary optic neuropathy (LHON). Six eyes of four patients with LHON underwent SD-OCT (optical coherence tomography) at month 1, 3, 6 and 12 after visual loss. In two eyes, the examination was carried out in the presymptomatic stage. The relationship and curves for area under the receiver operator characteristic (AUROC) were generated to assess the ability of each parameter to detect ganglion cell loss. Significant longitudinal thinning of GC-IPL and mRNFL was detected in LHON. GC-IPL thinning was detectable in the deviation map during the presymptomatic stage in the inner ring of the nasal sector and then it progressively extended following a centrifugal and spiral pattern. Similarly, mRNFL thinning began in the inferonasal sector and it progressively extended. No further statistically significant changes were detected...