Isolation of Drosophila melanogaster Testes

The testes of Drosophila melanogaster provide an important model for the study of stem cell maintenance and differentiation, meiosis, and soma-germline interactions. Testes are typically isolated from adult males 0-3 days after eclosion from the pupal case. The testes of wild-type flies are easily distinguished from other tissues because they are yellow, but the testes of white mutant flies, a common genetic background for laboratory experiments are similar in both shape and color to the fly gut. Performing dissection on a glass microscope slide with a black background makes identifying the testes considerably easier. Testes are removed from the flies using dissecting needles. Compared to protocols that use forceps for testes dissection, our method is far quicker, allowing a well-practiced individual to dissect testes from 200-300 wild-type flies per hour, yielding 400-600 testes. Testes from white flies or from mutants that reduce testes size are harder to dissect and typically yield 200-400 testes per hour

Role of ABCA7 loss-of-function variant in Alzheimer\u27s disease: A replication study in European–Americans

INTRODUCTION: A recent study found a significant increase of ABCA7 loss-of-function variants in Alzheimer’s disease (AD) cases compared to controls. Some variants were located on noncoding regions, but it was demonstrated that they affect splicing. Here, we try to replicate the association between AD risk and ABCA7 loss-of-function variants at both the single-variant and gene level in a large and well-characterized European American dataset. METHODS: We genotyped the GWAS common variant and four rare variants previously reported for ABCA7 in 3476 European–Americans. RESULTS: We were not able to replicate the association at the single-variant level, likely due to a lower effect size on the European American population which led to limited statistical power. However, we did replicate the association at the gene level; we found a significant enrichment of ABCA7 loss-of-function variants in AD cases compared to controls (P = 0.0388; odds ratio =1.54). We also confirmed that the association of the loss-of-function variants is independent of the previously reported genome-wide association study signal. CONCLUSIONS: Although the effect size for the association of ABCA7 loss-of-function variants with AD risk is lower in our study (odds ratio = 1.54) compared to the original report (odds ratio = 2.2), the replication of the findings of the original report provides a stronger foundation for future functional applications. The data indicate that different independent signals that modify risk for complex traits may exist on the same locus. Additionally, our results suggest that replication of rare-variant studies should be performed at the gene level rather than focusing on a single variant

Mitogenome characterization and diversity of the nangqian grey yak (bos grunniens)

Nangqian grey yak (Bos grunniens) is a unique yak population in Qinghai Province, China. In this study, the whole mitogenome sequences of 18 Nangqian grey yaks were sequenced based on the next-generation sequencing (NGS) technology and annotated. The total length of whole mitogenome sequence is between 16.323 bp and 16.325 bp, including a non-coding control region (D-loop region), 22 tRNA genes, 13 protein-coding genes and two rRNA genes (12S rRNA and 16S rRNA). Maternal genetic diversity based on the mitogenome variations was analyzed. A total of 12 haplotypes were identified among 18 complete mitogenome sequences, the haplotype diversity and nucleotide diversity of Nangqian grey yak were 0.948±0.033 and 0.001±0.001, respectively. Compared with the wild yak population and six other domestic yak breeds/populations in China, the haplotype diversity of Nangqian grey yak population was higher, indicating abundant maternal genetic diversity in Nangqian grey yak. The phylogenetic tree showed that Nangqian grey yak was most closely related to Tibet alpine, Xueduo, Changtai, Sibu, Zhongdian, Tianzhu white, Ashdan, Jinchuan, Jiulong, Pamir, Pali, Qinghai plateau, Huanhu, Datong, Bazhou and wild yak breeds/populations, closer to Chawula, Muli, Gannan, Niangya and Yushu yak breeds, but far away from other yak breeds (i.e. Leiwuqi and Maiwa yak)

Chitinase-3-like 1 protein (CHI3L1) locus influences cerebrospinal fluid levels of YKL-40

BACKGROUND: Alzheimer’s disease (AD) pathology appears several years before clinical symptoms, so identifying ways to detect individuals in the preclinical stage is imperative. The cerebrospinal fluid (CSF) Tau/Aβ(42) ratio is currently the best known predictor of AD status and cognitive decline, and the ratio of CSF levels of chitinase-3-like 1 protein (CHI3L1, YKL-40) and amyloid beta (Aβ(42)) were reported as predictive, but individual variability and group overlap inhibits their utility for individual diagnosis making it necessary to find ways to improve sensitivity of these biomarkers. METHODS: We used linear regression to identify genetic loci associated with CSF YKL-40 levels in 379 individuals (80 cognitively impaired and 299 cognitively normal) from the Charles F and Joanne Knight Alzheimer’s Disease Research Center. We tested correlations between YKL-40 and CSF Tau/Aβ(42) ratio, Aβ(42), tau, and phosphorylated tau (ptau(181)). We used studentized residuals from a linear regression model of the log-transformed, standardized protein levels and the additive reference allele counts from the most significant locus to adjust YKL-40 values and tested the differences in correlations with CSF Tau/Aβ(42) ratio, Aβ(42), tau, and ptau(181). RESULTS: We found that genetic variants on the CH13L1 locus were significantly associated with CSF YKL-40 levels, but not AD risk, age at onset, or disease progression. The most significant variant is a reported expression quantitative trait locus for CHI3L1, the gene which encodes YKL-40, and explained 12.74 % of the variance in CSF YKL-40 in our study. YKL-40 was positively correlated with ptau(181) (r = 0.521) and the strength of the correlation significantly increased with the addition of genetic information (r = 0.573, p = 0.006). CONCLUSIONS: CSF YKL-40 levels are likely a biomarker for AD, but we found no evidence that they are an AD endophenotype. YKL-40 levels are highly regulated by genetic variation, and by including genetic information the strength of the correlation between YKL-40 and ptau(181) levels is significantly improved. Our results suggest that studies of potential biomarkers may benefit from including genetic information. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12883-016-0742-9) contains supplementary material, which is available to authorized users

Writing in London. Home and Languaging in the Work of London Poets of Chinese Descent

This essay discusses literary works produced in London by poets of Chinese descent who are foreign-born or London native. Some of these works are written in English, and some in Chinese. The aim is to discuss poetry that has emphatically or reluctantly embraced the identity narrative, talking of home and belonging in substantially different ways from each other, according to each poet’s individual relationship with movement, migration, and stability. Therefore, through the use of the phrase ‘London poets of Chinese descent’, I do not aim at tracing a shared sense of identity, but instead I am interested in using London as a method for an oblique reading that recognises the variety of angles and approaches in these poets’ individual experience, history and circumstances that can range from occasional travel to political exile

Metatranscriptomic analysis revealed Prevotella as a potential biomarker of oropharyngeal microbiomes in SARS-CoV-2 infection

Background and objectivesDisease severity and prognosis of coronavirus disease 2019 (COVID-19) disease with other viral infections can be affected by the oropharyngeal microbiome. However, limited research had been carried out to uncover how these diseases are differentially affected by the oropharyngeal microbiome of the patient. Here, we aimed to explore the characteristics of the oropharyngeal microbiota of COVID-19 patients and compare them with those of patients with similar symptoms.MethodsCOVID-19 was diagnosed in patients through the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by quantitative reverse transcription polymerase chain reaction (RT-qPCR). Characterization of the oropharyngeal microbiome was performed by metatranscriptomic sequencing analyses of oropharyngeal swab specimens from 144 COVID-19 patients, 100 patients infected with other viruses, and 40 healthy volunteers.ResultsThe oropharyngeal microbiome diversity in patients with SARS-CoV-2 infection was different from that of patients with other infections. Prevotella and Aspergillus could play a role in the differentiation between patients with SARS-CoV-2 infection and patients with other infections. Prevotella could also influence the prognosis of COVID-19 through a mechanism that potentially involved the sphingolipid metabolism regulation pathway.ConclusionThe oropharyngeal microbiome characterization was different between SARS-CoV-2 infection and infections caused by other viruses. Prevotella could act as a biomarker for COVID-19 diagnosis and of host immune response evaluation in SARS-CoV-2 infection. In addition, the cross-talk among Prevotella, SARS-CoV-2, and sphingolipid metabolism pathways could provide a basis for the precise diagnosis, prevention, control, and treatment of COVID-19

Genome-wide association study identifies four novel loci associated with Alzheimer's endophenotypes and disease modifiers

More than 20 genetic loci have been associated with risk for Alzheimer's disease (AD), but reported genome-wide significant loci do not account for all the estimated heritability and provide little information about underlying biological mechanisms. Genetic studies using intermediate quantitative traits such as biomarkers, or endophenotypes, benefit from increased statistical power to identify variants that may not pass the stringent multiple test correction in case-control studies. Endophenotypes also contain additional information helpful for identifying variants and genes associated with other aspects of disease, such as rate of progression or onset, and provide context to interpret the results from genome-wide association studies (GWAS). We conducted GWAS of amyloid beta (Aβ42), tau, and phosphorylated tau (ptau181) levels in cerebrospinal fluid (CSF) from 3146 participants across nine studies to identify novel variants associated with AD. Five genome-wide significant loci (two novel) were associated with ptau181, including loci that have also been associated with AD risk or brain-related phenotypes. Two novel loci associated with Aβ42 near GLIS1 on 1p32.3 (β = -0.059, P = 2.08 × 10-8) and within SERPINB1 on 6p25 (β = -0.025, P = 1.72 × 10-8) were also associated with AD risk (GLIS1: OR = 1.105, P = 3.43 × 10-2), disease progression (GLIS1: β = 0.277, P = 1.92 × 10-2), and age at onset (SERPINB1: β = 0.043, P = 4.62 × 10-3). Bioinformatics indicate that the intronic SERPINB1 variant (rs316341) affects expression of SERPINB1 in various tissues, including the hippocampus, suggesting that SERPINB1 influences AD through an Aβ-associated mechanism. Analyses of known AD risk loci suggest CLU and FERMT2 may influence CSF Aβ42 (P = 0.001 and P = 0.009, respectively) and the INPP5D locus may affect ptau181 levels (P = 0.009); larger studies are necessary to verify these results. Together the findings from this study can be used to inform future AD studies

Inverted Lymphoglandular Polyp in Descending Colon

A 47-year-old male with a history of left colon cancer, status post left colon resection for 12 years, presented with rectal bleeding. Colonoscopic examination revealed an 8 mm sessile polyp in the proximal descending colon. Microscopic examination showed that the surface of this polyp was covered with a layer of normal colonic mucosa with focal surface erosion. In the submucosal layer, an intimate admixture of multiple cystically dilated glands and prominent lymphoid aggregates with germinal centers was seen. The glands were lined by columnar epithelium. Immunohistochemical staining showed the glands were positive for CK20 and CDX2 and negative for CK7, with a low proliferative index, mostly consistent with reactive colonic glands. The patient remained asymptomatic after one-year follow-up. A review of the literature shows very rare descriptions of similar lesions, but none fits exactly this pattern. We would designate this inverted lymphoglandular polyp and present this case to raise the awareness of recognizing this unusual histological entity

Physicochemical Properties and Cookie-Making Performance as Fat Replacer of Wax-Based Rice Bran Oil Oleogels

Reducing the intake of trans and saturated fatty acids is a trend in healthy eating. In this study, the oleogels were prepared from rice bran oil (RBO), candle wax (CDW), beeswax (BW), rice bran wax (RBW), and carnauba wax (CRW), respectively, and the results based on their physicochemical properties and crystal structures at critical concentrations, 6 wt.%, 8 wt.%, and 10 wt.%, were determined to further investigate the oleogels as a shortening substitute in cookie recipes. Oleogel has a smooth, spreadable β′ crystal shape which creates excellent sensory properties and improves the texture, but also has some economic benefits. A comparison between the oleogels formed at critical concentrations and those with improved mass fractions was performed in several analyses such as PLM and texture, and the oleogels with higher mass fractions had a greater hardness and stickiness and denser crystal structures. This study was used to optimize the cookie recipe by partially replacing shortening with oleogel and preparing the cookies according to the 0:1, 3:7, 1:1, 7:3, 1:0 oleogel shortening mixture, respectively. Based on the results of the textural analysis, a colorimetric and sensory evaluation of the optimized formulation of oleogels in cookies, it was evident that BW and RBW oleogels have more potential to replace shortening in cookies than CDW and CRW oleogels. In particular, oleogels with a concentration of 6 wt.% RBW (RBW-6) and at a 7:3 (oleogel:shortening) shortening replacement exhibited a hardness and crispness of 15.75 N and 97.73 g, respectively, with an L* value of 66.66 and a sensory score of 22.32 ± 0.09. The value for the color perception difference (dE) between the cookies and the control group was −3.73, which allowed us to obtain a good product with a quality and characteristics similar to shortening. This supports the feasibility of new solid fats to replace traditional plastic fats in baked goods