Gender Identification and Classification of Drosophila melanogaster Flies Using Machine Learning Techniques

Drosophila melanogaster is an important genetic model organism used extensively in medical and biological studies. About 61% of known human genes have a recognizable match with the genetic code of Drosophila flies, and 50% of fly protein sequences have mammalian analogues. Recently, several investigations have been conducted in Drosophila to study the functions of specific genes exist in the central nervous system, heart, liver, and kidney. The outcomes of the research in Drosophila are also used as a unique tool to study human-related diseases. This article presents a novel automated system to classify the gender of Drosophila flies obtained through microscopic images (ventral view). The proposed system takes an image as input and converts it into grayscale illustration to extract the texture features from the image. Then, machine learning (ML) classifiers such as support vector machines (SVM), Naive Bayes (NB), and K -nearest neighbour (KNN) are used to classify the Drosophila as male or female. The proposed model is evaluated using the real microscopic image dataset, and the results show that the accuracy of the KNN is 90%, which is higher than the accuracy of the SVM classifier.

Emodin reduces tumor burden by diminishing M2-like macrophages in colorectal cancer

Emodin, a natural anthraquinone, has been shown to have anti-tumorigenic properties and may be an effective therapy for colorectal cancer (CRC). However, its clinical development has been hampered by a poor understanding of its mechanism of action. The purpose of this study was to 1) evaluate the efficacy of emodin in mouse models of intestinal/colorectal cancer and 2) to examine the impact of emodin on macrophage behavior in the context of CRC. We utilized a genetic model of intestinal cancer (ApcMin/+) and a chemically induced model of CRC (AOM/DSS). Emodin was administered orally (40 mg/kg or 80 mg/kg in AOM/DSS and 80mg/kg in ApcMin/+) 3x/week to observe its preventative effects. Emodin reduced polyp count and size in both rodent models (p<0.05). We further analyzed the colon microenvironment of AOM/DSS mice and found that mice treated with emodin exhibited lower pro-tumorigenic M2-like macrophages and a reduced ratio of M2/M1 macrophages within the colon (p<0.05). Despite this, we did not detect any significant changes in M2-associated cytokines (IL10, IL4, and Tgfb1) nor M1-associated cytokines (IL6, TNFα, IL1β, and IFNγ) within excised polyps. However, there was a significant increase in NOS2 expression (M1 marker) in mice treated with 80 mg/kg emodin (p<0.05). To confirm emodin's effects on macrophages, we exposed bone marrow-derived macrophages (BMDMs) to C26 colon cancer cell conditioned media. Supporting our in vivo data, emodin reduced M2-like macrophages. Overall, these data support the development of emodin as a natural compound for prevention of CRC given its ability to target pro-tumor macrophages.

The dgc2 gene encoding di-guanylate cyclase suppresses both motility and biofilm formation in the filamentous cyanobacterium Leptolyngbya boryana.

Colony pattern formations of bacteria with motility manifest complicated morphological self-organization phenomena. Leptolyngbya boryana is the filamentous cyanobacterial species, which has been used as a genetic model organism for studying metabolism including photosynthesis and nitrogen-fixation. Although a widely used type strain (wild type) of this species has not been reported to show any motile activity, we isolated a spontaneous mutant strain which shows active motility (gliding activity) to give rise to complicated colony patters, including comet-like wandering clusters and disk-like rotating vortices on solid media. Whole-genome resequencing identified multiple mutations on the genome in the mutant strain. We confirmed that inactivation of a candidate gene, dgc2 (LBDG_02920), in the wild type background was sufficient to give rise to motility and the morphological colony patterns. This gene encodes a protein, containing the GGDEF motif, which is conserved at the catalytic domain of diguanylate cyclase (DGC). Although DGC has been reported to be involved in biofilm formation, the mutant strain lacking dgc2 significantly facilitated biofilm formation, suggesting a role of DGC for suppressing both gliding motility and biofilm formation. Thus, L. boryana provides an excellent genetic model to study dynamic colony pattern formation, and novel insight on a role of c-di-GMP for biofilm formation.

Behavioral and Gene Regulatory Responses to Developmental Drug Exposures in Zebrafish

Developmental consequences of prenatal drug exposure have been reported in many human cohorts and animal studies. The long-lasting impact on the offspring—including motor and cognitive impairments, cranial and cardiac anomalies and increased prevalence of ADHD—is a socioeconomic burden worldwide. Identifying the molecular changes leading to developmental consequences could help ameliorate the deficits and limit the impact. In this study, we have used zebrafish, a well-established behavioral and genetic model with conserved drug response and reward pathways, to identify changes in behavior and cellular pathways in response to developmental exposure to amphetamine, nicotine or oxycodone. In the presence of the drug, exposed animals showed altered behavior, consistent with effects seen in mammalian systems, including impaired locomotion and altered habituation to acoustic startle. Differences in responses seen following acute and chronic exposure suggest adaptation to the presence of the drug. Transcriptomic analysis of exposed larvae revealed differential expression of numerous genes and alterations in many pathways, including those related to cell death, immunity and circadian rhythm regulation. Differential expression of circadian rhythm genes did not correlate with behavioral changes in the larvae, however, two of the circadian genes, arntl2 and per2, were also differentially expressed at later stages of development, suggesting a long-lasting impact of developmental exposures on circadian gene expression. The immediate-early genes, egr1, egr4, fosab, and junbb, which are associated with synaptic plasticity, were downregulated by all three drugs and in situ hybridization showed that the expression for all four genes was reduced across all neuroanatomical regions, including brain regions implicated in reward processing, addiction and other psychiatric conditions. We anticipate that these early changes in gene expression in response to drug exposure are likely to contribute to the consequences of prenatal exposure and their discovery might pave the way to therapeutic intervention to ameliorate the long-lasting deficits.

Male and female recombination landscapes of diploid Arabidopsis arenosa

The number and placement of meiotic crossover events during meiosis has important implications for the fidelity of chromosome segregation as well as patterns of inheritance. Despite the functional importance of recombination, recombination landscapes vary widely among and within species, and this can have a strong impact on evolutionary processes. A good knowledge of recombination landscapes is important for model systems in evolutionary and ecological genetics, since it can improve interpretation of genomic patterns of differentiation and genome evolution, and provides an important starting point for understanding the causes and consequences of recombination rate variation. Arabidopsis arenosa is a powerful evolutionary genetic model for studying the molecular basis of adaptation and recombination rate evolution. Here we generate genetic maps for two diploid A. arenosa individuals from distinct genetic lineages where we have prior knowledge that meiotic genes show evidence of selection. We complement the genetic maps with cytological approaches to map and quantify recombination rates, and test the idea that these populations might have distinct patterns of recombination. We explore how recombination differs at the level of populations, individuals, sexes and genomic regions. We show that the positioning of crossovers along a chromosome correlates with their number, presumably a consequence of crossover interference, and discuss how this effect can cause differences in recombination landscape among sexes or species. We identify several instances of female segregation distortion. We found that averaged genome-wide recombination rate is lower and sex differences subtler in A. arenosa than in A. thaliana.

Association of Rs13118928 and Rs1828591 Polymorphisms in HHIP Gene with COPD Susceptibility: A Meta-Analysis of Case-Control Studies

In recent years, investigators have been striving to explore the pathogenesis of chronic obstructive pneumonia disease (COPD). Hedgehog Interacting Protein (HHIP) has been identified as a candidate susceptibility gene. Our aim is to synthesize and include all evidences to get a more comprehensive result. We searched 6 online databases- PubMed, Web of Science, Cochrane Library, Wanfang, EMBASE, CNKI. All included studies were published before October 1, 2021. We used Newcastle-Ottawa scale (NOS) to evaluate the bias of each study. Meta-analysis methods were conducted to evaluate the pooled result. A total of 14 comparative studies were included in this meta-analysis, for rs13118928 polymorphism, significant associations were observed in 5 genetic models, (A vs. G, OR=1.18, 95CI%=[1.07-1.30], P=0.0006; AA vs. GG, OR=1.56, 95CI%=[1.22-2.00], P=0.0004; AG vs. GG, OR=1.28, 95CI%=[1.05-1.55], P=0.01; AA+AG vs. GG, OR=1.36, 95CI%=[1.12-1.65], P=0.002; AA vs. AG+GG, OR=1.18, 95CI%=[1.05-1.33], P=0.006). as for rs1828591, there were also significant associations detected in the overall population, (A vs. G, OR=1.12, 95CI%=[1.05-1.19], P=0.0003; AA vs. GG, OR=1.27, 95CI%=[1.04-1.56], P=0.02; AG vs. GG, OR=1.25, 95CI%=[1.03-1.51], P=0.02; AA+AG vs. GG, OR=1.26, 95CI%=[1.04-1.53], P=0.02; AA vs. AG+GG, OR=1.10, 95CI%=[1.01-1.19], P=0.03). This meta-analysis showed that the A allele in both rs13118928 and rs1828591 was turn out to be the risk allele in developing COPD. The result of Codominant genetic model, Dominant genetic model and Recessive genetic model remain the same.

Analysis of Drosophila cardiac hypertrophy by micro-computerized tomography for genetic dissection of heart growth mechanisms

Heart failure is often preceded by pathological cardiac hypertrophy, a thickening of the heart musculature driven by complex gene regulatory and signaling processes. The Drosophila heart has great potential as a genetic model for deciphering the underlying mechanisms of cardiac hypertrophy. However, current methods for evaluating hypertrophy of the Drosophila heart are laborious and difficult to carry out reproducibly. Here we demonstrate that micro-computerized tomography (microCT) is an accessible, highly reproducible method for non-destructive, quantitative analysis of Drosophila heart morphology and size. To validate our microCT approach for analyzing Drosophila cardiac hypertrophy, we show that expression of constitutively active Ras (Ras85DV12), previously shown to cause hypertrophy of the fly heart, results in significant thickening of both adult and larval heart walls when measured from microCT images. We then show using microCT analysis that genetic upregulation of store-operated Ca2+ entry (SOCE) driven by expression of constitutively active Stim (StimCA) or Orai (OraiCA) proteins also results in significant hypertrophy of the Drosophila heart, through a process that specifically depends on Orai Ca2+ influx channels. Intravital imaging of heart contractility revealed significantly reduced end diastolic and systolic dimensions in StimCA and OraiCA expressing hearts, consistent with the hypertrophic phenotype. These results demonstrate that increased SOCE activity is an important driver of hypertrophic cardiomyocyte growth, and demonstrate how microCT analysis combined with tractable genetic tools in Drosophila can be used to delineate molecular signaling processes that underlie cardiac hypertrophy and heart failure.

Tracing fluid evolution in sedimentary basins with calcite geochemical, isotopic and U-Pb geochronological data: Implications for petroleum and mineral resource accumulation in the Nanpanjiang Basin, South China

Fluid migration in sedimentary basins enable mass and energy transport and play critical roles in geochemical and geodynamical evolution of sedimentary basins. Moreover, reconstructing sedimentary basin fluid evolution from the geological record aids in constraining the evolution of associated petroleum and mineralization systems. As a relict of fluid flow activity, calcite is often a record of fluid flow and therefore can be used to characterize the fluids responsible for its precipitation. Here we study the Nanpanjiang Basin in South China where petroleum reservoirs and Carlin-type gold deposits spatially coincide. Through in situ U-Pb dating and geochemical analysis (87Sr/86Sr, δ18OVienna standard mean ocean water, δ13CVienna Peedee belemnite, rare earth elements) of calcite, this work constrains the key times related to petroleum migration/accumulation and Carlin-type gold mineralization, defines the basin fluid evolution, and proposes a genetic model for petroleum accumulation and gold mineralization within the Nanpanjiang Basin. The U-Pb age (ca. 241.4 Ma) for the gray/black calcite related to bitumen indicates the petroleum migration/accumulation occurred during the Triassic. The U-Pb date (ca. 106−121 Ma) of the white calcite associated with the gold-bearing pyrite, realgar, and fluorite record the lower timing limit of the Carlin-type gold systems. The geochemical data suggest both calcite types are cogenetic but suffered complex evolution with the gray/black calcite precipitating under low temperatures related to the continuous basin burial and the white calcite affected by post formation alteration related to both hydrothermal and meteoric fluids. Combined with the regional tectonic history, the Early Triassic petroleum migration/accumulation and the Early Cretaceous secondary Carlin-type gold mineralization events are considered to be related to the collision between the Indo-China and South China blocks, and the subduction between the Paleo-Pacific and Eurasian plates, respectively.

Association of CDKAL1 RS10946398 Gene Polymorphism with Susceptibility to Diabetes Mellitus Type 2: A Meta-Analysis

Background. Diabetes is one of the common chronic diseases in which susceptibility is determined by a combination of genetic and environmental factors, and more than 90% of diabetic patients are diabetes mellitus type 2 (T2DM). The existing studies on the association between CDKAL1 rs10946398 gene polymorphism and susceptibility to type 2 diabetes are inconsistent across populations. Aim. We aim to explore the association between CDKAL1 rs10946398 gene polymorphism and susceptibility to type 2 diabetes in different populations. Methods. We examined all studies before June 12, 2021, that associated CDKAL1 rs10946398 with T2DM. Heterogeneity was assessed by meta-analysis of allelic inheritance models (A vs. C), dominant inheritance models (AA vs. AC+CC), and recessive inheritance model (AA+AC vs. CC); I 2 was used to assess the heterogeneity (if I 2 < 50 %, the fixed-effects model was used; if I 2 ≥ 50 %, the random-effects model was used for data consolidation); correlation was judged by a forest map; potential publication bias was tested by the Egger test ( p > 0.05 indicates that there is no publication bias). Results. Fourteen data totaling 30288 subjects, including 19272 controls and 11016 patients with T2DM, met our inclusion criteria. In the Asian population, the differences were statistically significant ( p < 0.01 ) for dominant genetic model ( OR = 0.75 , 95 % CI = 0.64 -0.88, p = 0.0003 ). But the allelic effect model ( OR = 0.87 , 95 % CI = 0.75 -1.02, p = 0.08 ) and the recessive genetic model ( OR = 0.85 , 95 % CI = 0.66 -1.10, p = 0.23 ) were not statistically significant ( p > 0.01 ). In the non-Asian population, the differences were statistically significant ( p < 0.01 ) for the allelic effect model ( OR = 0.83 , 95 % CI = 0.77 -0.88, p < 0.00001 ), the dominant model ( OR = 0.79 , 95 % CI = 0.72 -0.87, p < 0.00001 ), and the recessive model ( OR = 0.78 , 95 % CI = 0.70 -0.87, p < 0.0001 ). Conclusion. In this study, CDKAL1 RS10946398 was positively associated with T2DM, but the association was different in Asian populations.

Potential Contribution of IL-27 and IL-23 Gene Polymorphisms to Multiple Sclerosis Susceptibility: An Association Analysis at Genotype and Haplotype Level

(1) Background: interleukin 23 (IL-23) and interleukin 27 (IL-27) modulate the activity of T helper 17 cells (Th17) with critical roles in autoimmune diseases and multiple sclerosis (MS). The genes responsible for cytokine generation are highly influenced by the presence of single nucleotide polymorphisms (SNP) in main regions such as regulatory sequences or in promoter regions, contributing to disease susceptibility and evolution. The present study analyzed the associations of IL-23 and IL-27 SNPs with susceptibility to multiple sclerosis. (2) Methods: We performed a case-control study including 252 subjects: 157 patients diagnosed with MS and 95 controls. We used polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) to determine the genotypes for IL-27 T4730С (rs 181206), IL-27 A964G (rs 153109), and IL-23 receptor gene (IL-23R) G1142A (rs 11209026). (3) Results: The IL27-T4730С gene polymorphism was significantly associated with an increased odds of MS under the dominant genetic model (TC + CC variant genotypes, adjusted odds ratio OR = 4.06, 95% CI: 2.14–7.83, p-value = 0.000007, Q-value = 0.000063). Individuals carrying the IL-27 A924G variant (AG + GG) genotype presented higher odds of MS compared to non-carriers under the dominant model (adjusted OR = 1.93, 95% CI: 1.05–3.51, p-value = 0.0324, Q-value = 0.05832) and the allelic genetic model (unadjusted p-value = 0.015, OR = 1.58, 95% CI: 1.09–2.28), while IL-23-R381Q SNP conferred a decreased odds of MS under a codominant model of inheritance (adjusted OR = 0.26, 95% CI: 0.08–0.92, p-value = 0.0276, Q-value = 0.058) and an allelic model (unadjusted p-value = 0.008, OR = 0.23, 95% CI: 0.07–0.75). In an additive model with adjustment for age group (≤40 years vs. >40 years), sex and smoking, patients carrying the G-C (A964G, T4730C) haplotype had a 3.18 increased risk (95% CI: 1.74–5.81, p < 0.001) to develop multiple sclerosis. (4) Conclusions: The results of the current study showed a significant relationship of IL-27-A964G and IL-27-T4730C polymorphisms with increased risk of MS, and also the protective role of the IL-23-R381Q polymorphism. Moreover, the haplotype-based analysis proposed the mutant G-C (A924G, T4730C) as a significant risk haplotype for the development of MS.