Genetic Introgression Between Different Groups Reveals the Differential Process of Asian cultivated Rice

Genetic introgression plays an important role in the domestication of crops. The Asian cultivate rice consists of two major subspecies, they are indica and japonica. There are already many reports about existence of genetic introgression between the two subspecies. However, those studies often use few limited markers to characterize the genetic introgression that exists in some specific small populations. In this study we use the genome wide variation data of Asia cultivated rice to investigate their genetic introgression on the whole genome level. We detect a total of 13 significantly high introgression loci between the tropical japonica and indica population. Two different methods are used to identify the genetic introgression regions. For most of the detected introgression regions they generally get consistent results. Some previous known introgression genes are detected in the identified introgression loci, such as heat resistance gene TT1 and GLW7. The biological functions for these genetic introgression regions are annotated by the published QTL mapping results. We find that genetic introgression plays an important role in both the determination of the phenotype and the domestication process of different groups. Our study also provides useful information and resources for the study of rice gene function and domestication process.

KAJIAN PENURUNAN KADAR BESI (FE) PADA AIR SUMUR GALI MENGGUNAKAN METODE FILTRASI DENGAN VARIASI BESARAN BILANGAN IODINE PADA KARBON AKTIF

<p>Dermonganti hamlet, Ketitang village, Jumo Sub-distric, Temanggung distric is the area which most of the people use dug well water. The result from the three parameters that are tested. They are TDS, Ph, and iron rate (Fe) that is obtain from the result of iron rate (Fe) 2,56mg/l, 2,525mg/l 2,69 mg/L. The result is more than 1 mg/l means that exceeding the quality standards of maximum limit from the regulation of Minister of Health of the Indonesian Republic number 32 in the year 2017. So, dug well water processing is required through the filtration to reduce iron rate (Fe). The research used a tubular filtration contains a filter media that are sands, pumice, active carbon that have the magnitude of each iodine is 650mg/l, 800mg/l, 1000mg/l with each filter media thickness is 30cm. Parameter reviewed is iron rate (Fe). The processing is carried out with contact time 1 hour, 2 hours, 3hours for every variation. Data analysis used are regression analysis and Anova test. The result of filtration shows the highest removal value of iron rate (Fe) occurs to the 1 unit filtration with 1 hour contact time. The iron rate removal score (Fe) at 1 hour used filter 1 with the sand, pumice and active carbon as filter medias with the iodine number 1000mg/g with the percentage 59,17%. The greater its iodine number of activated carbon shows the increasing value of removal iron rate content.</p><strong>Key words:</strong> Iodine number, Filtration, Iron rate.

Biological variation data for kidney function related parameter: serum beta trace protein, creatinine and cystatin C from 22 apparently healthy Turkish subjects

Objectives Biological variation is defined as the variation in analytical concentration between and within individuals, and being aware of this biological variation is important for understanding disease dynamics. The aim of our study is to calculate the within-subject (CVI) and between-subject (CVG) biological variations of serum creatinine, cystatin C and Beta trace protein (BTP), as well as the reference change value (RCV) and individuality indexes (II), which are used to calculate the glomerular filtration rate while evaluating kidney damage. Methods Blood samples were collected from 22 healthy volunteers for 10 consecutive weeks and stored at −80 °C until the day of analysis. While the analysis for serum creatinine was performed colorimetrically with the kinetic jaffe method, the nephelometric method was employed for cystatin C and BTP measurements. All analyses were carried out in a single session for each test. Results Analytical coefficient of variation (CVA) for serum creatinine, cystatin C and beta trace protein was 5.56, 3.48 and 5.37%, respectively. CVI and CVG: for serum creatinine: 3.31, 14.50%, respectively, for cystatin C: 3.15, 12.24%, respectively, for BTP: 9.91, 14.36%, respectively. RCV and II were calculated as 17.94%, 0.23 for serum creatinine, 13.01%, 0.26 for cystatin C, 31.24%, 0.69 for BTP, respectively. Conclusions According to the data obtained in our study, serum creatinine and cystatin C show high individuality, therefore we think that the use of RCV instead of reference ranges would be appropriate. Although II is found to be low for BTP, more studies are needed to support this finding.

Variations of Movement, Dispersal, and Morphometrics among Subpopulations of Javan Endemic Damselfly, Drepanosticta spatulifera (Odonata: Platystictidae) in Petungkriyono Forest

Drepanosticta spatulifera is a Javan endemic damselfly. The population is spread unevenly in the Petungkriyono Forest and is threatened due to environmental pressure. The aims of this research are to know the variation of the movement, dispersal, and morphometric among subpopulations of D. spatulifera. Movement and dispersal variation data collection was done using Mark Release Recapture (MRR) for six weeks from early August until mid-September 2020. The collection of morphometric samples was done during the last week of the MRR survey and 46 individuals were measured with 12 continuous characters. During the MRR survey, 596 males of D. spatulifera were marked and 302 were recaptured. D. spatulifera had short movement and dispersal thus no individuals were found across the subpopulations. The distance moved of successive capture and net lifetime movement were dominantly less or equal to five meters. The duration of the MRRsurvey had a low correlation with the dispersal distance of D. spatulifera. In themorphometric variations, closer subpopulations tended to have a similar cluster ofmorphometric characters. Variation of distance moved between successive captureand wing size from Mangli Stream was significantly different from other sites. Thesubpopulation of Mangli, the farthest and higher altitude of the sites, had thehighest distance move, more disperse, and the largest wing size. Our study showedthat D. spatulifera was extremely sedentary damselfly. It will enhance inbreeding andvulnerability to extinction. Therefore, the interaction between the subpopulationsof D. spatulifera in the Petungkriyono Forest needs to be done more.

Migrations of cancer cells through the lens of phylogenetic biogeography

Malignant cells leave their initial tumor of growth and disperse to other tissues to form metastases. Dispersals also occur in nature when individuals in a population migrate from their area of origin to colonize other habitats. In cancer, phylogenetic biogeography is concerned with the source and trajectory of cell movements. We examine the suitability of primary features of organismal biogeography, including genetic diversification, dispersal, extinction, vicariance, and founder effects, to describe and reconstruct clone migration events among tumors. We used computer-simulated data to compare fits of seven biogeographic models and evaluate models’ performance in clone migration reconstruction. Models considering founder effects and dispersals were often better fit for the clone phylogenetic patterns, especially for polyclonal seeding and reseeding of metastases. However, simpler biogeographic models produced more accurate estimates of cell migration histories. Analyses of empirical datasets of basal-like breast cancer had model fits consistent with the patterns seen in the analysis of computer-simulated datasets. Our analyses reveal the powers and pitfalls of biogeographic models for modeling and inferring clone migration histories using tumor genome variation data. We conclude that the principles of molecular evolution and organismal biogeography are useful in these endeavors but that the available models and methods need to be applied judiciously.

Pan-Cancer Analysis of Genomic and Prognostic Characteristics Associated With Coronavirus Disease 2019 Regulators

Background: Cancer patients are alleged to have poor coronavirus disease 2019 (COVID-19) outcomes. However, no systematic or comprehensive analyses of the role and mechanisms of COVID-19 receptor-related regulators in cancer are available.Methods: We comprehensively evaluated the genomic alterations and their clinical relevance of six COVID-19 receptor-related regulators [transmembrane serine protease 2 (TMPRSS2), angiotensinogen (AGT), angiotensin-converting enzyme 1 (ACE1), solute carrier family 6 member 19 (SLC6A19), angiotensin-converting enzyme 2 (ACE2), and angiotensin II receptor type 2 (AGTR2)] across a broad spectrum of solid tumors. RNA-seq data, single nucleotide variation data, copy number variation data, methylation data, and miRNA–mRNA interaction network data from The Cancer Genome Atlas (TCGA) of 33 solid tumors were analyzed. We assessed the sensitivities of drugs targeting COVID-19 receptor-related regulators, using information from the Cancer Therapeutics Response Portal database.Results: We found that there are widespread genetic alterations of COVID-19 regulators and that their expression levels were significantly correlated with the activity of cancer hallmark-related pathways. Moreover, COVID-19 receptor-related regulators may be used as prognostic biomarkers. By mining the genomics of drug sensitivities in cancer databases, we discovered a number of potential drugs that may target COVID-19 receptor-related regulators.Conclusion: This study revealed the genomic alterations and clinical characteristics of COVID-19 receptor-related regulators across 33 cancers, which may clarify the potential mechanism between COVID-19 receptor-related regulators and tumorigenesis and provide a novel approach for cancer treatments.

Hydration Kinetics for Alkaline Activation of Slag from Color Variation Data

In this study, we explore a new method based on color variation data to derive the kinetics of the entire process of the hydration of alkali-activated slag (AAS). Using this image analysis technique, we can monitor the induction period that cannot be observed using conventional microcalorimetry techniques. Color variation was recorded across a sequence of 9999 images, which were processed via MATLAB software package. Further, an average pixel value (APV) was determined to represent the color in each image. Reaction parameters, such as color variation velocity v(t), reaction speed ε(t), and hydration degree α(t), that govern the entire hydration process were determined. On the basis of the reaction parameters and a Krstulovic–Dabic kinetic model, integral and differential equations were derived to simulate the three basic processes of AAS hydration. Equations describing the reaction kinetics of AAS with solutions of three different concentrations of NaOH were extracted using this method.

LocalVar: a local variant collection manager to asynchronously detect synonyms, HGVS expression changes, and variant interpretation changes from ClinVar

While there are several public repositories of biological sequence variation data and associated annotations, there is little open-source tooling designed specifically for the upkeep of local collections of variant data. Many clinics curate and maintain such local collections and are burdened by frequent changes in the representation of those variants and evolving interpretations of clinical significance. A dictionary of genetic variants from the Huntsman Cancer Institute was analyzed over a period of two years and used to inform the development of LocalVar. This tool is institution-agnostic and uses publicly available ClinVar files to provide the following functionality: auto-complete search bar to pre-empt duplicate entries; single or bulk new variant record entry; auto-detection and merge suggestions for duplicate variant records; auto-detection and merge suggestions for variant records with HGVS expressions that are marked as synonyms in ClinVar; asynchronous suggestion of HGVS expression or variant interpretation updates; history tracking of additions, merges, updates, or other manual edits made to variant records; and the easy export of the collection (.csv), edit history (.json), or HGVS synonym bins (.json).