Search

ATP6V1B2 pathogenic variants are linked with variable phenotypes, such as dominant deafness-onychodystrophy syndrome (DDOD), autosomal dominant Zimmermann-Laband syndrome type 2 (ZLS2), and some cases of DOORS (deafness, onychodystrophy, osteodystrophy, intellectual disability [ID], and seizures). Epilepsy was first linked to ATP6V1B2, when the p.(Glu374Gln) missense variant was detected in a patient with ID and seizures, but without characteristic features of DDOD or ZLS2 syndromes. We herein report a novel pathogenic ATP6V1B2:p.Glu374Gly variant detected in an adult patient with ID and myoclonic-atonic seizures. The (re)occurrence of different variants affecting the same highly conserved hydrophilic glutamic acid on position 374 of the V-proton ATPase subunit B, indicates a potential novel pathogenic hotspot and a critical role for the specific residue in the development of epilepsy. ATP6V1B2 gene defects should be considered when analyzing patients with epilepsy, even in the absence of most cardinal features of DDOD, DOORS, or ZLS such as deafness, onychodystrophy, and osteodystrophy.

Numerous factors influence breast cancer (BC) prognosis, thus complicating the prediction of outcome. By identifying biomarkers that would distinguish the cases with poorer response to therapy already at the time of diagnosis, the rate of survival could be improved. Lately, Piwi‐interacting RNAs (piRNAs) have been introduced as potential cancer biomarkers, however, due to the recently raised challenges in piRNA annotations, further evaluation of piRNAs’ involvement in cancer is required. We performed small RNA sequencing in 227 fresh‐frozen breast tissue samples from the Eastern Finnish Kuopio Breast Cancer Project material to study the presence of piRNAs in BC and their associations with the clinicopathological features and outcome of BC patients. We observed the presence of three small RNAs annotated as piRNA database entries (DQ596932, DQ570994, and DQ571955) in our samples. The actual species of these RNAs however remain uncertain. All three small RNAs were upregulated in grade III tumors and DQ596932 additionally in estrogen receptor negative tumors. Furthermore, patients with estrogen receptor positive BC and higher DQ571955 had shorter relapse‐free survival and poorer BC‐specific survival, thus indicating DQ571955 as a candidate predictive marker for radiotherapy response in estrogen receptor positive BC. DQ596932 showed possible prognostic value in BC, whereas DQ570994 was identified as a candidate predictive marker for tamoxifen and chemotherapy response. These three small RNAs appear as candidate biomarkers for BC, which could after further investigation provide novel approaches for the treatment of therapy resistant BC. Overall, our results indicate that the prevalence of piRNAs in cancer is most likely not as comprehensive as has been previously thought., We have observed three small RNAs associating with clinical characteristics and patient outcome in breast cancer. The actual species of these RNAs needs further clarification but these results indicate that the dysregulation of piRNAs in cancer is most likely not as general a phenomenon as has been previously thought.

The synthesis of a fully deprotected Kdo-containing rhamnogalacturonan II pentasaccharide is described. The strategy relies on the preparation of a suitably protected homogalacturonan tetrasaccharide backbone through a post-glycosylation oxidation approach, and its stereoselective glycosylation with a Kdo fluoride donor.

3‐Methylglutaconic (3MGC) aciduria is a common phenotypic feature of a growing number of inborn errors of metabolism. “Primary” 3MGC aciduria is caused by deficiencies in leucine pathway enzymes while “secondary” 3MGC aciduria results from inborn errors of metabolism that impact mitochondrial energy production. The metabolic precursor of 3MGC acid is trans‐3MGC CoA, an intermediate in the leucine catabolism pathway. Gas chromatography‐mass spectrometry (GC‐MS) analysis of commercially available trans‐3MGC acid yielded a mixture of cis and trans isomers while 1H‐NMR spectroscopy of trans‐3MGC acid at 25°C provided no evidence for the cis isomer. When trans‐3MGC acid was incubated under conditions used for sample derivatization prior to GC‐MS (but with no trimethylsilane added), 1H‐NMR spectroscopy provided evidence of trans to cis isomerization. Incubation of trans‐3MGC acid at 37°C resulted in time‐dependent isomerization to cis‐3MGC acid. Cis‐3MGC acid behaved in a similar manner except that, under identical incubation conditions, less isomerization occurred. In agreement with these experimental results, molecular modeling studies provided evidence that the energy minimized structure of cis‐3MGC acid is 4 kJ/mol more stable than that for trans‐3MGC acid. Once generated in vivo, trans‐3MGC acid is proposed to isomerize via a mechanism involving π electron delocalization with formation of a resonance structure that permits bond rotation. The data presented are consistent with the occurrence of both diastereomers in urine samples of subjects with 3MGC aciduria.

BACKGROUND There are scarce data on the hypomineralisation of other permanent teeth (HOPT) than the index teeth of Molar Incisor Hypomineralisation (MIH). AIM To report on the prevalence and surface pattern of HOPT and seek associations with MIH. DESIGN Representative samples of urban Greek 14-year-olds were examined in classroom with a dental mirror. Their enamel defects were recorded using EAPD criteria for MIH. Descriptive statistics and correlation tests for HOPT vs previously reported MIH findings in the same samples were applied. RESULTS HOPT prevalence in 1156 consented adolescents was 22.9%. 148 (16.2%) of 912 no-MIH children had HOPT; 117 (48.1%) of the 244 MIH children had HOPT too (OR 3.0, 95% CI 2.4-3.6). There were more HOPT teeth per child in the MIH vs no-MIH children (P

Background High tumor mutation burden is shown to be associated with a poor clinical outcome. As the tumor‐derived fraction of circulating cell‐free DNA (cfDNA) is shown to reflect the genetic spectrum of the tumor, we examined whether the mutation burden of cfDNA could be used to predict the clinical outcomes of early‐stage breast cancer (BC) patients. Methods We selected a set of 79 Finnish early‐stage BC cases with a good prognosis based on traditional prognostic parameters but some of which still developed relapsed disease during follow‐up. cfDNA was isolated from the serum collected at the time of diagnosis, sequenced, and compared to matched primary tumors, clinical parameters, and survival data. Results High cfDNA mutation burden was associated with the poor relapse‐free survival (RFS) (P = .016, HR = 2.23, 95% Cl 1.16‐4.27) when patients were divided into high and low mutation burden according to the median number of somatic variants. A high discordance was observed between the matched tumor and cfDNA samples, thus highlighting the challenges related to the liquid biopsy of early‐stage cancer cases. Despite the low number of detected tumor‐specific variants, the presence of tumor‐specific somatic variants in the cfDNA was associated with the poor RFS (P = .009, HR = 2.31, 95% Cl 1.23‐4.31). Conclusions Our results confirm previously observed challenges about the accuracy of liquid biopsy‐based genotyping of early‐stage cancers and support the parallel sequencing of tumor and cfDNA while also demonstrating how the presence of tumor‐specific somatic variants and the high mutation burden in the cfDNA are both associated with the poor RFS, thus indicating the prognostic potential of liquid biopsy in the context of early‐stage cancers., High mutation burden and the presence of tumor‐specific mutations in circulating cell‐free DNA in early‐stage breast cancer patients were observed to be associated with a poor relapse‐free survival. Our results suggest that the liquid biopsy of early‐stage cancers might provide potential benefits when making primary prognosis despite the challenges that are associated with the liquid biopsy of early‐stage cancers.

Oligomannose-type glycans on the spike protein of HIV-1 constitute relevant epitopes to elicit broadly neutralizing antibodies (bnAbs). Herein we describe an improved synthesis of α- and β-linked hepta- and nonamannosyl ligands that, subsequently, were converted into BSA and CRM(197) neoglycoconjugates. We assembled the ligands from anomeric 3-azidopropyl spacer glycosides from select 3-O-protected thiocresyl mannoside donors. Chain extensions were achieved using [4+3] or [4+5] block synthesis of thiocresyl and trichloroacetimidate glycosyl donors. Subsequent global deprotection generated the 3-aminopropyl oligosaccharide ligands. ELISA binding data obtained with the β-anomeric hepta- and nonamannosyl conjugates with a selection of HIV-1 bnAbs showed comparable binding of both mannosyl ligands by Fab fragments yet lesser binding of the nonasaccharide conjugate by the corresponding IgG antibodies. These results support previous observations that a complete Man(9) structure might not be the preferred antigenic binding motif for some oligomannose-specific antibodies and have implications for glycoside designs to elicit oligomannose-targeted HIV-1-neutralizing antibodies.

BACKGROUND The use of pulmonary function tests (PFTs) in infants has increased during the last decades, making the need for equipment- and ethnic-specific reference data mandatory for appropriate interpretation of the results. AIM Our aim was to investigate how well the already published reference equations for infant spirometry fit a healthy population of Swedish infants. METHOD We performed forced tidal and raised volume expiratory maneuvers in healthy infants using Jaeger BabyBody equipment. RESULTS PFT data were collected from 91 healthy infants aged between 3 months to 2 years at 143 occasions. Mean (standard deviation) z-scores were 0.68(1.33) for maximal flow at functional residual capacity (V'max FRC), -0.15(0.96) for forced vital capacity (FVC), 0.40(1.33) for the forced expired volume in the initial 0.5 seconds (FEV0.5 ) and 0.52(0.93) for the ratio FEV0.5 /FVC, respectively. Z-scores for all indices but FEV0.5 /FVC were highly dependent on length. CONCLUSIONS We have shown that the use of previously published reference equations may result in an age-related misinterpretation of lung function measure in a Swedish infant population.

The rise of inexpensive, user-friendly cameras and editing software promises to revolutionize data collection with minimal disturbance to marine mammals. Video sequences recorded by aerial drones and GoPro cameras provided close-up views and unique perspectives of humpback whales engulfing juvenile salmon at or just below the water surface in Southeast Alaska and Prince William Sound. Although humpback feeding is famous for its flexibility, several stereotyped events were noted in the 47 lunges we analyzed. Engulfment was rapid (mean 2.07 s), and the entrance through which the tongue inverts into the ventral pouch was seen as water rushes in. Cranial elevation was a major contributor to gape, and pouch contraction sometimes began before full gape closure, with reverberating waves indicating rebounding flow of water within the expanded pouch. Expulsion of filtered water began with a small splash at the anterior of the mouth, followed by sustained excurrent flow in the mouth's central or posterior regions. Apart from a splash of rebounding water, water within the mouth was surprisingly turbulence-free during engulfment, but submersion of the whale's head created visible surface whirlpools and vortices which may aggregate prey for subsequent engulfment.

Previous genome-wide association studies among women of European ancestry identified two independent breast cancer susceptibility loci represented by single nucleotide polymorphisms (SNPs) rs13281615 and rs11780156 at 8q24. A fine-mapping study across 2.06 Mb (chr8:127,561,724-129,624,067, hg19) in 55,540 breast cancer cases and 51,168 controls within the Breast Cancer Association Consortium was conducted. Three additional independent association signals in women of European ancestry, represented by rs35961416 (OR = 0.95, 95% CI = 0.93-0.97, conditional p = 5.8 × 10(-6) ), rs7815245 (OR = 0.94, 95% CI = 0.91-0.96, conditional p = 1.1 × 10(-6) ) and rs2033101 (OR = 1.05, 95% CI = 1.02-1.07, conditional p = 1.1 × 10(-4) ) were found. Integrative analysis using functional genomic data from the Roadmap Epigenomics, the Encyclopedia of DNA Elements project, the Cancer Genome Atlas and other public resources implied that SNPs rs7815245 in Signal 3, and rs1121948 in Signal 5 (in linkage disequilibrium with rs11780156, r(2) = 0.77), were putatively functional variants for two of the five independent association signals. The results highlighted multiple 8q24 variants associated with breast cancer susceptibility in women of European ancestry.

The present study comprises the second part of an ongoing study focusing on olive oil from five less well-known Greek cultivars for three of which there are no data available in the literature regarding their chemical composition. A total of 74 olive oil samples were collected during the harvesting periods 2012–2013 and 2013–2014. Headspace-solid phase microextraction was applied to determine the olive oil volatile profile. Fifty-six compounds were identified and semi-quantified by CG–MS. Furthermore, fatty acid composition, conventional quality parameters and color parameters were determined in an effort to characterize and differentiate olive oils according to cultivar. All samples were characterized as extra virgin olive oils. Data obtained showed significant differences between the cultivars. Multi-element analysis in combination with chemometrics resulted in a high classification rate of 86.5 % for the combination of volatiles plus color, 89.2 % for the combination of VC plus FA, and 91.9 % for the combination of FA composition plus color plus CQP.

Background Antley-Bixler syndrome (ABS) is an exceptionally rare craniosynostosis syndrome that can be accompanied by disordered steroidogenesis, and is mainly caused by mutations in the POR gene, inherited in an autosomal recessive manner. Here we report the prenatal and postmortem findings of three sibling fetuses with ABS as a result of compound heterozygosity of a paternal submicroscopic deletion and a maternal missense mutation in the POR gene. Methods Prenatal ultrasound and postmortem examination were performed in three sibling fetuses with termination of pregnancy at 22, 23, and 17 weeks of gestation, respectively. Molecular analysis of fetus 2 and 3 included (a) bidirectional sequencing of exon 8 of the POR gene after amplification of the specific locus by polymerase chain reaction, to detect single nucleotide variants (SNVs) and (b) high resolution comparative genomic hybridization (CGH) positive single nucleotide polymorphism array CGH (aCGH) analysis to detect copy number variants (CNVs), copy neutral areas of loss of heterozygosity and uniparental disomy. Results The diagnosis of ABS was suggested by the postmortem examination findings. The combination of the POR gene molecular analysis and aCGH revealed a compound heterozygous genotype of a maternal SNV (p.A287P) and a paternal CNV (NC_000007.13:g.(?_75608488)_(75615534_?)del). Conclusion To the best of our knowledge, these sibling fetuses add to the few reported cases of ABS, caused by a combination of a SNV and a CNV in the POR gene. The detailed description of the pathologic and radiographic findings of second trimester fetuses affected with ABS adds novel knowledge concerning the early ABS phenotype, in lack of previous relevant reports. Birth Defects Research (Part A) 106:536–541, 2016. © 2016 Wiley Periodicals, Inc.

Chromosomal microarray analysis (CMA) is currently considered a first-tier diagnostic assay for the investigation of autism spectrum disorders (ASD), developmental delay and intellectual disability of unknown etiology. High-resolution arrays were utilized for the identification of copy number variations (CNVs) in 195 ASD patients of Greek origin (126 males, 69 females). CMA resulted in the detection of 65 CNVs, excluding the known polymorphic copy number polymorphisms also found in the Database of Genomic Variants, for 51/195 patients (26.1%). Parental DNA testing in 20/51 patients revealed that 17 CNVs were de novo, 6 paternal and 3 of maternal origin. The majority of the 65 CNVs were deletions (66.1%), of which 5 on the X-chromosome while the duplications, of which 7 on the X-chromosome, were rarer (22/65, 33.8%). Fifty-one CNVs from a total of 65, reported for our cohort of ASD patients, were of diagnostic significance and well described in the literature while 14 CNVs (8 losses, 6 gains) were characterized as variants of unknown significance and need further investigation. Among the 51 patients, 39 carried one CNV, 10 carried two CNVs and 2 carried three CNVs. The use of CMA, its clinical validity and utility was assessed.

Volatile compound (VC) analysis and fatty acids (FA) composition in combination with statistical analysis [Multivariate Analysis of Variance/Linear Discriminant Analysis (MANOVA/LDA)] were used for the differentiation of extra virgin olive oils (EVOO) according to cultivar. A total of 104 olive oil samples from six Greek cultivars were collected during the harvesting period 2012–2013. Fifty-six VC were identified and semi-quantified by Head Space-Solid Phase Microextraction-Gas Chromatography/Mass Spectrometry (HS-SPME-GC/MS). FA composition was determined by Gas Chromatography-Flame Ionization Detector (GC-FID). The application of MANOVA/LDA to total VC and FA showed that 34 VC and 9 FA were significant for the differentiation of olive oil cultivar. Based on volatiles’ analysis a classification rate of 83.0% was achieved. The respective classification rate for FA analysis was 92.1% while that of the combination of VC and FA was 93%. Practical applications: This research documents that VC and FA composition could play an important role in the differentiation of cultivar origin of EVOO. Furthermore, researchers had the opportunity to study the characteristics of some less-known olive oil varieties such as Galano from Chalkidiki and Samothraki from Samothraki island. The results obtained may aid toward the labelling as “Protected Designation of Origin” (PDO) or “Protected Geographical Indication” (PGI) for EVOO from these olive cultivars. Differentiation of Greek olive oil samples according to cultivar based on instrumental analysis and chemometrics.

The ketosidic linkage of 3‐deoxy‐d‐manno‐octulosonic acid (Kdo) to lipid A constitutes a general structural feature of the bacterial lipopolysaccharide core. Glycosylation reactions of Kdo donors, however, are challenging due to the absence of a directing group at C‐3 and elimination reactions resulting in low yields and anomeric selectivities of the glycosides. While 3‐iodo‐Kdo fluoride donors showed excellent glycosyl donor properties for the assembly of Kdo oligomers, glycosylation of N‐acetyl‐glucosamine derivatives was not straightforward. Specifically, oxazoline formation of a β‐anomeric methyl glycoside, as well as iodonium ion transfer to an allylic aglycon was found. In addition, dehalogenation of the directing group by hydrogen atom transfer proved to be incompatible with free hydroxyl groups next to benzyl groups. In contrast, glycosylation of a suitably protected methyl 2‐acetamido‐2‐deoxy‐α‐d‐glucopyranoside derivative and subsequent deiodination proceeded in excellent yields and α‐specificity, and allowed for subsequent 4‐O‐phosphorylation. This way, the disaccharides α‐Kdo‐(2→6)‐α‐GlcNAcOMe and α‐Kdo‐(2→6)‐α‐GlcNAcOMe‐4‐phosphate were obtained in good overall yields.

Aims High amounts of tumour-associated macrophages (TAMs) and hyaluronan (HA) correlate with tumour aggressiveness in breast cancer, but the relationship between these parameters is unclear. The aim of this study was to assay the numbers of TAMs in 278 human breast cancer cases, and their correlations with HA-related factors, clinical variables, and outcome. Methods and results The immunoreactivities for CD163 and CD68 were considered as indicators for M2-like and all TAMs, respectively. The numbers of TAMs were counted in at least four hot spots, and averaged to represent the numbers of TAMs in each section. In the statistical analyses, the numbers were graded as either low or high according to the median. High numbers of TAMs correlated with a high tumour HA content, HA synthases, CD44 positivity, and poor outcome. The number of CD163-positive cells represented a strong independent prognostic factor. There was also a significant correlation between obesity and a high number of CD163-positive cells. Conclusions Concurrent increases in TAMs and HA in breast cancer indicate that the accumulation of HA facilitates macrophage infiltration and inflammatory responses during human breast cancer progression.

Breast cancer risk factors and clinical outcomes vary by tumour marker expression. However, individual studies often lack the power required to assess these relationships, and large-scale analyses are limited by the need for high throughput, standardized scoring methods. To address these limitations, we assessed whether automated image analysis of immunohistochemically stained tissue microarrays can permit rapid, standardized scoring of tumour markers from multiple studies. Tissue microarray sections prepared in nine studies containing 20 263 cores from 8267 breast cancers stained for two nuclear (oestrogen receptor, progesterone receptor), two membranous (human epidermal growth factor receptor 2 and epidermal growth factor receptor) and one cytoplasmic (cytokeratin 5/6) marker were scanned as digital images. Automated algorithms were used to score markers in tumour cells using the Ariol system. We compared automated scores against visual reads, and their associations with breast cancer survival. Approximately 65-70% of tissue microarray cores were satisfactory for scoring. Among satisfactory cores, agreement between dichotomous automated and visual scores was highest for oestrogen receptor (Kappa = 0.76), followed by human epidermal growth factor receptor 2 (Kappa = 0.69) and progesterone receptor (Kappa = 0.67). Automated quantitative scores for these markers were associated with hazard ratios for breast cancer mortality in a dose-response manner. Considering visual scores of epidermal growth factor receptor or cytokeratin 5/6 as the reference, automated scoring achieved excellent negative predictive value (96-98%), but yielded many false positives (positive predictive value = 30-32%). For all markers, we observed substantial heterogeneity in automated scoring performance across tissue microarrays. Automated analysis is a potentially useful tool for large-scale, quantitative scoring of immunohistochemically stained tissue microarrays available in consortia. However, continued optimization, rigorous marker-specific quality control measures and standardization of tissue microarray designs, staining and scoring protocols is needed to enhance results.