Normal variations in brain oxygen extraction fraction are partly attributed to differences in end-tidal CO2

Cerebral oxygen extraction fraction is an important physiological index of the brain's oxygen consumption and supply and has been suggested to be a potential biomarker for a number of diseases such as stroke, Alzheimer's disease, multiple sclerosis, sickle cell disease, and metabolic disorders. However, in order for oxygen extraction fraction to be a sensitive biomarker for personalized disease diagnosis, inter-subject variations in normal subjects must be minimized or accounted for, which will otherwise obscure its interpretation. Therefore, it is essential to investigate the physiological underpinnings of normal differences in oxygen extraction fraction. This work used two studies, one discovery study and one verification study, to examine the extent to which an individual's end-tidal CO₂ can explain variations in oxygen extraction fraction. It was found that, across normal subjects, oxygen extraction fraction is inversely correlated with end-tidal CO₂. Approximately 50% of the inter-subject variations in oxygen extraction fraction can be attributed to end-tidal CO₂ differences. In addition, oxygen extraction fraction was found to be positively associated with age and systolic blood pressure. By accounting for end-tidal CO₂, age, and systolic blood pressure of the subjects, normal variations in oxygen extraction fraction can be reduced by 73%, which is expected to substantially enhance the utility of oxygen extraction fraction as a disease biomarker.

Year effects: Interannual variation as a driver of community assembly dynamics

Environmental conditions that vary from year to year can be strong drivers of ecological dynamics, including the composition of newly assembled communities. However, ecologists often chalk such dynamics up to "noise" in ecological experiments. Our lack of attention to such "year effects" hampers our understanding of contingencies in ecological assembly mechanisms and limits the generalizability of research findings. Here, we provide examples from published research demonstrating the importance of year effects during community assembly across study systems. We further quantify these year effects with two case studies-a grassland restoration experiment and a study of postfire conifer recruitment-finding that the effects of initiation year on community composition can dictate community as much, if not more, than the effects of experimental treatments or site. The evidence strongly suggests that year effects are pervasive and profound, and that year effects early in community assembly can drive strong and enduring divergence in community structure and function. Explicit attention to year effects in ecological research serves to illuminate basic ecological principles, allowing for better understanding of contingencies in ecology. These dynamics also have strong implications for applied ecological research, offering new insights into ecological restoration as well as future climate change.

The Identity of Organisms in Scientific Practice: Integrating Historical and Relational Conceptions

We address the identity of biological organisms at play in experimental and modeling practices. We first examine the central tenets of two general conceptions, and we assess their respective strengths and weaknesses. The historical conception, on the one hand, characterizes organisms' identity by looking at their past, and specifically at their genealogical connection with a common ancestor. The relational conception, on the other hand, interprets organisms' identity by referring to a set of distinctive relations between their parts, and between the organism and its environment. While the historical and relational conceptions are understood as opposed and conflicting, we submit that they are also fundamentally complementary. Accordingly, we put forward a hybrid conception, in which historical and relational (and more specifically, organizational) aspects of organisms' identity sustain and justify each other. Moreover, we argue that organisms' identity is not only hybrid but also bounded, insofar as the compliance with specific identity criteria tends to vanish as time passes, especially across generations. We spell out the core conceptual framework of this conception, and we outline an original formal representation. We contend that the hybrid and bounded conception of organisms' identity suits the epistemological needs of biological practices, particularly with regards to the generalization and reproducibility of experimental results, and the integration of mathematical models with experiments.

Variation in Patient Smoking Cessation Rates Among Health-Care Providers: An Observational Study

BACKGROUND

Physicians play a crucial role in providing smoking cessation counseling and medications. However, it is unknown whether individual physicians' approaches affect whether patients quit.

RESEARCH QUESTION

This study assessed patient quit rates within a national quality-improvement learning collaborative to document variation in quit rates at the physician, practice, and health system levels.

STUDY DESIGN AND METHODS

A retrospective cohort study was conducted of primary care patients identified from the Optum analytics database containing longitudinal ambulatory data for patients from 22 health-care organizations between January 2012 and December 2018. The study included smokers aged ≥ 18 years who attended at least three ambulatory visits, with two visits at least 1 year apart. The primary study outcome was abstinence for ≥ 1 year. A mixed effects logistic regression model was used to predict the probability of quitting as a function of patient variables. Quit rates were then adjusted by patient factors and calculated at the level of clinician, clinic/practice, and health system.

RESULTS

Across all systems, 56% of patients had a documented smoking status in 2017. Among nearly 1 million smokers, 24% quit smoking. In the regression model, patient characteristics associated with quitting included older age, Hispanic ethnicity, being married, urban residence, commercial insurance, pregnancy, and a diagnosis of pneumonia, myocardial infarction, ischemic heart disease, cataract, or asthma. Medicaid insurance, low income, high BMI, peripheral vascular disease, alcohol-related diagnosis, and COPD were negatively associated with smoking cessation. Adjusted quit rates ranged from 14.3% to 34.5% across 20 health systems, 5% to 66% among 1,399 practice sites, and 4% to 87% among 3,803 health-care providers. Of smokers, 10.2% were prescribed smoking deterrents, and 3.9% were referred for counseling.

INTERPRETATION

Smoking cessation rates varied substantially at the practitioner, practice site, and health system levels. It is likely that individual physician approaches to smoking cessation influence patients' likelihood of quitting.

Contributing factors to the plasma albumin level at diagnosis of hematological malignancy

OBJECTIVES

Many factors contribute to the plasma albumin (PA) level. We aimed to quantify different factors' relative contribution to the PA level when diagnosing hematological malignancy (HM).

METHODS

The study was a population-based registry study including patients with HM in a Danish region. We applied multivariate linear regression analyses with C-reactive protein (CRP), WHO performance score (WHO-PS), age, sex, comorbidity, and HM type as exposures and the PA level on the day of the HM diagnosis (DX) as the outcome. The relative contribution of each exposure was determined as a percentage of the models' coefficient of determination (R²).

RESULTS

In total, 2528 patients with HM had PA measured on DX. In the model comprising all exposures, CRP contributed with 65.8% to the R² of 0.389 whereas 3 variables (CRP, WHO-PS, HM type) together contributed with 96.1%. When CRP was excluded from the model, R² declined to 0.215 and the WHO-PS contributed with 96%. Other models, including separate analyses for each HM type, corroborated these results, except in myeloma patients where WHO-PS contributed with 61.1% to the R² of 0.234.

CONCLUSION

The inflammation biomarker CRP was the main predictor of the PA level on DX. The WHO-PS also contributed to the PA level on DX whereas the remaining factors (HM type, age, sex, and comorbidity) were of much less importance.

The Branching and Innervation Pattern of the Radial Nerve in the Forearm: Clarifying the Literature and Understanding Variations and Their Clinical Implications

BACKGROUND

This study attempted to clarify the innervation pattern of the muscles of the distal arm and posterior forearm through cadaveric dissection.

METHODS

Thirty-five cadavers were dissected to expose the radial nerve in the forearm. Each muscular branch of the nerve was identified and their length and distance along the nerve were recorded. These values were used to determine the typical branching and motor entry orders.

RESULTS

The typical branching order was brachialis, brachioradialis, extensor carpi radialis longus, extensor carpi radialis brevis, supinator, extensor digitorum, extensor carpi ulnaris, abductor pollicis longus, extensor digiti minimi, extensor pollicis brevis, extensor pollicis longus and extensor indicis. Notably, the radial nerve often innervated brachialis (60%), and its superficial branch often innervated extensor carpi radialis brevis (25.7%).

CONCLUSIONS

The radial nerve exhibits significant variability in the posterior forearm. However, there is enough consistency to identify an archetypal pattern and order of innervation. These findings may also need to be considered when planning surgical approaches to the distal arm, elbow and proximal forearm to prevent an undue loss of motor function. The review of the literature yielded multiple studies employing inconsistent metrics and terminology to define order or innervation.

A Survey of Program Capacity and Skills of Florida Mosquito Control Districts to Conduct Arbovirus Surveillance and Control

Effective and efficient surveillance systems are key for preventing arthropod-borne diseases. We examined the capacity of Florida mosquito control districts (both state-approved and open programs, n = 90; 48.9% response rate). Questions centered on budgets, staffing levels, equipment, vector control measures, and staff perceptions of own agency's capacity to implement routine surveillance and vector control activities. Bivariate analyses indicate that districts with relatively large budgets have advanced capacities regarding staffing levels, employee specialties, mosquito control equipment, conduct routine surveillance and vector control yet they serve only a small proportion of the population. Independent tax districts' average annual budgets were 9 times higher than Board of County Commissioners programs in fiscal year 2017-18. Most respondents indicated that staff is appropriately trained, and has timely access to information and needed equipment for mosquito surveillance and control. Slightly more than half of respondents feel they are understaffed. Perceived understaffing may compromise mosquito surveillance and control efforts in some districts.

Identification of the Ovine Keratin-Associated Protein 2-1 Gene and Its Sequence Variation in Four Chinese Sheep Breeds

Keratin-associated proteins are important components of wool fibers. The gene encoding the high-sulfur keratin-associated protein 2-1 has been described in humans, but it has not been described in sheep. A basic local alignment search tool nucleotide search of the Ovine Genome Assembly version 4.0 using a human keratin-associated protein 2-1 gene sequence revealed a 399-base pair open reading frame, which was clustered among nine previously identified keratin-associated protein genes on chromosome 11. Polymerase chain reaction-single strand conformation polymorphism analysis revealed four different banding patterns, with these representing four different sequences (A-D) in Chinese sheep breeds. These sequences had the highest similarity to human keratin-associated protein 2-1 gene, suggesting that they represent variants of ovine keratin-associated protein 2-1 gene. Nine single nucleotide variations were detected in the gene, including one non-synonymous nucleotide substitution. Differences in variant frequencies between fine-wool sheep breeds and coarse-wool sheep breeds were detected. The gene was found to be expressed in various tissues, with the highest expression level in skin, and moderate expression levels in heart and lung tissue. These results reveal that the ovine keratin-associated protein 2-1 gene is variable and suggest the gene might affect variation in mean fiber diameter.

Human Cytomegalovirus Genomes Sequenced Directly From Clinical Material: Variation, Multiple-Strain Infection, Recombination, and Gene Loss

The genomic characteristics of human cytomegalovirus (HCMV) strains sequenced directly from clinical pathology samples were investigated, focusing on variation, multiple-strain infection, recombination, and gene loss. A total of 207 datasets generated in this and previous studies using target enrichment and high-throughput sequencing were analyzed, in the process enabling the determination of genome sequences for 91 strains. Key findings were that (i) it is important to monitor the quality of sequencing libraries in investigating variation; (ii) many recombinant strains have been transmitted during HCMV evolution, and some have apparently survived for thousands of years without further recombination; (iii) mutants with nonfunctional genes (pseudogenes) have been circulating and recombining for long periods and can cause congenital infection and resulting clinical sequelae; and (iv) intrahost variation in single-strain infections is much less than that in multiple-strain infections. Future population-based studies are likely to continue illuminating the evolution, epidemiology, and pathogenesis of HCMV.

Characterising Free-Range Layer Flocks Using Unsupervised Cluster Analysis

This study aimed to identify sub-populations of free-range laying hens and describe the pattern of their resource usage, which can affect hen performance and welfare. In three commercial flocks, 3125 Lohmann Brown hens were equipped with radio-frequency identification (RFID) transponder leg bands and placed with their flock companions, resulting in a total of 40,000 hens/flock. Hens were monitored for their use of the aviary system, including feeder lines, nest boxes, and the outdoor range. K-means and agglomerative cluster analysis, optimized with the Calinski-Harabasz Criterion, was performed and identified three clusters. Individual variation in time duration was observed in all the clusters with the highest individual differences observed on the upper feeder (140 ± 1.02%) and the range (176 ± 1.03%). Hens of cluster 1 spent the least amount time on the range and the most time on the feed chain located at the upper aviary tier (p < 0.05). We conclude that an uneven load on the resources, as well as consistent and inconsistent movement patterns, occur in the hen house. Further analysis of the data sets using classification models based on support vector machines, artificial neural networks, and decision trees are warranted to investigate the contribution of these and other parameters on hen performance.

An allelic variant of GAME9 determines its binding capacity with the GAME17 promoter in the regulation of steroidal glycoalkaloid biosynthesis in tomato

Steroidal glycoalkaloids (SGAs) are cholesterol-derived molecules found in the family Solanaceae. SGA content varies among different plant species and varieties. However, the genetic mechanisms regulating SGA content remain unclear. Here, we demonstrate that genetic variation in GLYCOALKALOID METABOLISM 9 (GAME9) is responsible for the variation in SGA content in tomato (Solanum lycopersicum). During a sequential analysis we found a 1 bp substitution in the AP2/ERF binding domain of GAME9. The 1 bp substitution in GAME9 was significantly associated with high SGA content and determined the binding capacity of GAME9 with the promoter of GAME17, a core SGA biosynthesis gene. The high-SGA GAME9 allele is mainly present in S. pimpinellifolium and S. lycopersicum var. cerasiforme populations and encodes a protein that can bind the GAME17 promoter. In contrast, the low-SGA GAME9 allele is mainly present in the big-fruited varieties of S. lycopersicum and encodes a protein that shows weak binding to the GAME17 promoter. Our findings provide new insight into the regulation of SGA biosynthesis and the factors that affect the accumulation of SGA in tomato.

Genome-Wide Association Study of Muscle Glycogen in Jingxing Yellow Chicken

Glucose metabolism plays an important role in many normal and pathological physiological processes in the body. The breakdown and synthesis of muscle glycogen provides ATP for muscle activities. A genome-wide association study for muscle glycogen was performed in 473 Jingxing yellow chickens to identify significant single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs) involved in muscle glycogen metabolism. A total of nine SNPs (p < 1/699341) and three INDELs (p < 1/755733) reached a significant level of potential association. The following results were obtained through a series of analyses, including additive effects and gene function annotation. Two significant SNPs were found in introns 12 and 13 of copine 4 (CPNE4) on chromosome 2. The wild-type and mutant individuals had significant differences in glycogen metabolism at two loci (p < 0.01 for both). Individuals carrying two mutations had increased muscle glycogen content. According to the gene annotation of chromosome 11, there is a significant INDEL in intron 6 of naked cuticle homolog 1 (NKD1). After the INDEL mutation, the glycogen content increased significantly. There was a significant difference between wild-type and mutant individuals (p < 0.01). These mutations likely affecting two genes (CPNE4 and NKD1) may affect glycogen storage in a pleiotropic manner. Gene annotation indicates that CPNE4 and NKD1 may affect the process of glucose metabolism. Our findings contribute to understanding the genetic regulation of muscle glycogen metabolism and provide theoretical support.

A Binary-Based Matrix Model for Malus Corolla Symmetry and Its Variational Significance

Floral symmetry (corolla symmetry) has important biological significance in plant genetics and evolution. However, it is often multi-dimensional and difficult to quantify. Here, we constructed a multi-dimensional data matrix [X Y Z] by extracting three qualitative variables with binary properties (X: corolla regularity of interval and coplanarity; Y: petal regularity of shape and size; Z: petal local regularity of curling and wrinkle) from different dimensions of petals (overall to individual, and then to the local): all petals (corolla), individual petals, and local areas of petals. To quantitatively express the degree of Malus corolla symmetry, these variables were then combined with weight assignments (X: 2² > Y: 2¹ > Z: 2⁰) based on their contributions to the corolla symmetry and the algorithm rule of converting binary to decimal values, which facilitated the unification of qualitative and quantitative analyses. Our results revealed significant reduction in degrees of Malus corolla symmetry along the direction of local to overall. Species showed higher degree of corolla symmetry than cultivars; however, taxa with stronger corolla symmetry might not necessarily be species. These findings provide new insights into the circumscription of Malus controversial species. The matrix model should be reference for future evaluation of angiosperm flower symmetry (lack of corolla fusion).

Variation Among Spirometry Interpretation Algorithms

Several algorithms exist to facilitate spirometric interpretation in clinical practice, yet there is a lack of consensus on how spirometric criteria for asthma, COPD, and restrictive disorders should be incorporated into spirometry interpretation algorithms suitable for use in day-to-day primary care management. The purpose of this review was to identify and describe the variability that exists among spirometry interpretation algorithms and how this might be relevant to the interpretation of spirometric data of common conditions encountered in primary care. MEDLINE, Embase, and mainstream search engines were used to identify all English-language spirometry interpretation algorithm-related material between January 1990 and December 2018. Eight variations in spirometry interpretation algorithms were identified via specific a priori assumptions that each spirometry interpretation algorithm should contain content consistent with national and international guidelines related to spirometry interpretation. Of the 26 spirometry interpretation algorithms identified, 5 were deemed impractical for day-to-day use in primary care (19%), 23 lacked a logic string leading to the postbronchodilator FEV₁/FVC (88%), 4 relied on postbronchodilator change in FEV₁ to distinguish between asthma and COPD (15%), 24 lacked a prompt for bronchodilator challenge when FEV₁/FVC was considered to be at a normal level (92%), 12 did not indicate whether the data represented a prebronchodilator or postbronchodilator scenario (46%), 7 did not include a logic string that considers mixed obstructive/restrictive defect (27%), 23 did not contain a prompt to refer for methacholine challenge testing when spirometry appeared normal (88%), and 2 spirometry interpretation algorithms did not include a logic string leading to restrictive disorder (8%). Our review suggests that there is considerable variability among spirometry interpretation algorithms available as diagnostic aids and that there is a need for standardization of spirometry interpretation algorithms in primary care.

Molecular characteristics of MC1R gene in tile-grey plumage of domestic chicken

1. Tile-grey plumage is a unique and rare feather type of local chicken breeds in China, but its genetic mechanism and corresponding genes remain unknown. 2. In order to identify the genetic basis and molecular characteristics of tile-grey plumage, this experiment investigated variations of melanocortin 1 receptor (MC1R) gene in Yunnan Piao chickens with typical tile-grey plumage characteristics in contrast with three Yunnan local breeds as well as two standard breeds with different plumage colour, and analysed the association between genic variation and tile-grey plumage. 3. Through sequencing and comparison of the entire coding region of the MC1R gene, a total of 10 SNP loci were detected, of which eight were non-synonymous mutations that cause amino acid changes. The gene frequency and genotype frequency of the MC1R mutation sites in different breeds and different plumage colour groups revealed that C69T, T212C and A274G were significantly associated with tile-grey plumage. Eighteen haplotypes of the MC1R gene were constructed based on 10 nucleotide variations and eight amino acid variations. Haplotype distribution and the median joining network in breeds and plumage colour groups revealed a main haplotype (hap2) for tile-grey plumage. Hap2 is unique to the tile-grey feather of Piao chicken, and the individuals carrying this haplotype account for 62.96% of the whole tile-grey chicken. 4. The results of this study are of significance for further analysis of the molecular basis of tile-grey plumage and the selective breeding of tile-grey plumage.

Effect of mean HbA1c on the association of HbA1c variability and all-cause mortality in patients with type 2 diabetes

AIM

To evaluate the effect of mean HbA1c on the correlation between HbA1c variability and all-cause mortality, and the risks associated with different levels of HbA1c and glycaemic control status in patients with type 2 diabetes.

MATERIALS AND METHODS

Patients with type 2 diabetes and at least three HbA1c measurements within 12-24 months were included. HbA1c variability score, coefficient of variation (CV) and standard deviation (SD) were used to evaluate variability. A variability score of 50 was set as a cutoff to define low and high variability.

RESULTS

A total of 4216 patients were included, of whom 1196 died during the observation period (11.1 ± 3.2 years). All-cause mortality increased with HbA1c variability score and the quartiles of HbA1c CV and SD. The strength of this association was attenuated after adjustment for mean HbA1c, and the risks associated with HbA1c variability and glycaemic control status were similar. The highest associated risk was observed with an HbA1c variability score of >50 and mean HbA1c of ≥7.5%. Mortality risk was significantly higher with a mean HbA1c of ≤6.0% and >8.5% and of ≤6.0% and >8.0% for low and high HbA1c variability, respectively.

CONCLUSIONS

Mean HbA1c contributed to the correlation between HbA1c variability and all-cause mortality. The risks associated with HbA1c variability and glycaemic control status were similar. The relationship between mean HbA1c and mortality presented a J-shaped distribution for both low and high HbA1c variability.

Variation and evolution of C:N ratio among different organs enable plants to adapt to N-limited environments

Carbon (C) and nitrogen (N) are the primary elements involved in the growth and development of plants. The C:N ratio is an indicator of nitrogen use efficiency (NUE) and an input parameter for some ecological and ecosystem models. However, knowledge remains limited about the convergent or divergent variation in the C:N ratios among different plant organs (e.g., leaf, branch, trunk, and root) and how evolution and environment affect the coefficient shifts. Using systematic measurements of the leaf-branch-trunk-root of 2,139 species from tropical to cold-temperate forests, we comprehensively evaluated variation in C:N ratio in different organs in different taxa and forest types. The ratios showed convergence in the direction of change but divergence in the rate of change. Plants evolved toward lower C:N ratios in the leaf and branch, with N playing a more important role than C. The C:N ratio of plant organs (except for the leaf) was constrained by phylogeny, but not strongly. Both the change of C:N during evolution and its spatial variation (lower C:N ratio at midlatitudes) help develop the adaptive growth hypothesis. That is, plants with a higher C:N ratio promote NUE under strong N-limited conditions to ensure survival priority, whereas plants with a lower C:N ratio under less N-limited environments benefit growth priority. In nature, larger proportion of species with a high C:N ratio enabled communities to inhabit more N-limited conditions. Our results provide new insights on the evolution and drivers of C:N ratio among different plant organs, as well as provide a quantitative basis to optimize land surface process models.

Maternal and Perinatal Factors Associated with the Human Milk Microbiome

Microbes are present in human milk regardless of the mother's health. The origins of the milk microbiota likely include the mother's skin, infant's mouth, and transfer from the maternal gastrointestinal (GI) tract. Prominent bacterial taxa in human milk are Staphylococcus and Streptococcus, but many other genera are also found including anaerobic Lactobacillus, Bifidobacterium, and Bacteroides. The milk microbiome is highly variable and potentially influenced by geographic location, delivery mode, time postpartum, feeding mode, social networks, environment, maternal diet, and milk composition. Mastitis alters the milk microbiome, and the intake of Lactobacilli has shown potential for mastitis treatment and prevention. Although milk and infant fecal microbiomes are different, their variations appear to be related - suggesting that milk is an important contributor of early GI colonization. Nonetheless, nothing is known regarding whether the milk microbiome influences infant health. Further research and clinical interventions are needed to determine if changes in the microbiomes of human milk and infant formula/food impact health.

Intralingual Variation in Acceptability Judgments and Production: Three Case Studies in Russian Grammar

This paper contributes to the task of defining the relationship between the results of production and rating experiments in the context of language variation. We address the following research question: how may the grammatical options available to a single speaker be distributed in the two domains of production and perception? We argue that previous studies comparing acceptability judgments and frequencies of occurrence suffer from significant limitations. We approach the correspondence of production and perception data by adopting an experimental design different from those used in previous research: (i) instead of using a corpus we use production data obtained experimentally from respondents who are later asked to make judgments, (ii) instead of pairwise phenomena we examine language variation, (iii) judgments are collected formally using the conditions and materials from the production experiment, (iv) we analyze the behavior of each participant across the production and acceptability judgment experiments. In particular, we examine three phenomena of variation in Russian: case variation in nominalizations, gender mismatch, and case variation in paucal constructions. Our results show that there is substantial alignment between acceptability ratings and frequency of occurrence. However, the distribution of frequencies and acceptability scores do not always correlate. Speakers are not consistent in choosing a single variant across the two types of experiment. Importantly, the types of inconsistency they display differ, which means that the variation can be characterized from this point of view. We conclude that the degree of coherence of the two experiments reflects the effects of the evolution of variation over time. Another result is that elicited production and acceptability judgments vary with respect to how they reveal variation in language. In the case of the development or disappearance of variants, production indicates this earlier than judgments, and the rating task has the effect of restricting the choices available to respondents. However, the production method should not thereby be considered more sensitive. We argue that only a combination of production and judgment data makes it possible to estimate the directionality of changes in variability and to see the full distribution of different variants.

Genome and Transcriptome Sequencing of casper and roy Zebrafish Mutants Provides Novel Genetic Clues for Iridophore Loss

casper has been a widely used transparent mutant of zebrafish. It possesses a combined loss of reflective iridophores and light-absorbing melanophores, which gives rise to its almost transparent trunk throughout larval and adult stages. Nevertheless, genomic causal mutations of this transparent phenotype are poorly defined. To identify the potential genetic basis of this fascinating morphological phenotype, we constructed genome maps by performing genome sequencing of 28 zebrafish individuals including wild-type AB strain, roy orbison (roy), and casper mutants. A total of 4.3 million high-quality and high-confidence homozygous single nucleotide polymorphisms (SNPs) were detected in the present study. We also identified a 6.0-Mb linkage disequilibrium block specifically in both roy and casper that was composed of 39 functional genes, of which the mpv17 gene was potentially involved in the regulation of iridophore formation and maintenance. This is the first report of high-confidence genomic mutations in the mpv17 gene of roy and casper that potentially leads to defective splicing as one major molecular clue for the iridophore loss. Additionally, comparative transcriptomic analyses of skin tissues from the AB, roy and casper groups revealed detailed transcriptional changes of several core genes that may be involved in melanophore and iridophore degeneration. In summary, our updated genome and transcriptome sequencing of the casper and roy mutants provides novel genetic clues for the iridophore loss. These new genomic variation maps will offer a solid genetic basis for expanding the zebrafish mutant database and in-depth investigation into pigmentation of animals.

Variations in gut bacterial communities between lesser white-fronted geese wintering at Caizi and Shengjin lakes in China

The avian gut microbiota plays an important role in shaping the health of its host. However, knowledge of gut bacteria in birds lags behind that of other animals. In this study, we investigated the gut bacterial communities of lesser white‐fronted geese (Anser erythropus) wintering at Shengjin Lake and Caizi Lake, China, using high‐throughput sequencing (Illumina MiSeq). Altogether, 1,053,624 high‐quality sequences and 4,405 operational taxonomic units (OTUs) were acquired from 30 fecal samples (15 per lake). The OTUs represented eight phyla and 17 classes from the Caizi Lake samples and seven phyla and 16 classes from the Shengjin Lake samples. Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla. The spatial distance and the Chao1, Simpson, and Shannon indices showed that the alpha diversity differed significantly between the samples from both lakes. The phylogenetic tree and heatmap analyses showed that all the Caizi Lake samples were clustered together and all the Shengjin Lake samples were clustered together. These findings suggest that diet may be an important driver of gut microbial community structure in the birds from each lake, and the obvious differentiation in their gut microbial structures may indicate that the bacteria are highly sensitive to food sources at both lakes.

The establishment of reference sequence for SARS-CoV-2 and variation analysis

Starting around December 2019, an epidemic of pneumonia, which was named COVID‐19 by the World Health Organization, broke out in Wuhan, China, and is spreading throughout the world. A new coronavirus, named severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) by the Coronavirus Study Group of the International Committee on Taxonomy of Viruses was soon found to be the cause. At present, the sensitivity of clinical nucleic acid detection is limited, and it is still unclear whether it is related to genetic variation. In this study, we retrieved 95 full‐length genomic sequences of SARAS‐CoV‐2 strains from the National Center for Biotechnology Information and GISAID databases, established the reference sequence by conducting multiple sequence alignment and phylogenetic analyses, and analyzed sequence variations along the SARS‐CoV‐2 genome. The homology among all viral strains was generally high, among them, 99.99% (99.91%‐100%) at the nucleotide level and 99.99% (99.79%‐100%) at the amino acid level. Although overall variation in open‐reading frame (ORF) regions is low, 13 variation sites in 1a, 1b, S, 3a, M, 8, and N regions were identified, among which positions nt28144 in ORF 8 and nt8782 in ORF 1a showed mutation rate of 30.53% (29/95) and 29.47% (28/95), respectively. These findings suggested that there may be selective mutations in SARS‐COV‐2, and it is necessary to avoid certain regions when designing primers and probes. Establishment of the reference sequence for SARS‐CoV‐2 could benefit not only biological study of this virus but also diagnosis, clinical monitoring and intervention of SARS‐CoV‐2 infection in the future.

In this study, we retrieved 95 full‐length genomic sequences of SARAS‐CoV‐2 strains, established the reference sequence, and analyzed sequencevariations along the SARS‐CoV‐2 genome. The homology among all viral strains was generally high. Although overall variation in ORF regions is low, 13 variation sites in 1a, 1b, S, 3a, M, 8, and N regions were identified, among which positions nt28144 in region 8 and nt8782 in ORF 1a showed mutation rate of 30.53% and 29.47% respectively.

Variation Patterns of the Volatiles during Germination of the Foxtail Millet (Setaria Italic): The Relationship between the Volatiles and Fatty Acids in Model Experiments

Functional and nutritional compounds are increased during foxtail millet germination while bad smell is produced due to the fatty acid oxidation. To eliminate the unpleasant aroma, the origins of the volatiles must be known. A comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry showed forty-nine volatiles containing 8 ketones, 10 aldehydes, 20 alkanes, 4 alcohols, 5 alkenes, and 2 furans were tentatively identified, and they increased during the germination of the foxtail millet. To identify the origin of some volatiles, model experiments by adding 6 fatty acids to the crude enzymes of the foxtail millet was designed, and 17 volatiles could be detected. The saturated fatty acids (palmitic acid and stearic acid) had no contributions to the formation of the volatiles, whereas the unsaturated fatty acid played important roles in the formation of volatiles. Among the unsaturated fatty acids, palmitoleic acid and linoleic acid produced most aldehydes, alcohols, and ketones, while linolenic acid produced the most alkanes and alkenes. This study will be helpful for controlling the smell of germinated seeds from the raw material selection.

MicroRNAs organize intrinsic variation into stem cell states

Understanding how mammalian organisms achieve the full diversity of cell types in the adult organism is a central goal of developmental cell biology. Recent work has shown that some embryonic precursor cells can self-organize into developmental structures but the mechanisms of gene regulation that contribute to this process remain unknown. Here we show embryonic stem cells self-organize into distinct gene expression states that resemble developmental gene programs. We find that microRNAs, small noncoding regulators of gene expression, play a critical role in organizing fluctuations across gene networks to help achieve this organization into distinct expression states.

Pluripotent embryonic stem cells (ESCs) contain the potential to form a diverse array of cells with distinct gene expression states, namely the cells of the adult vertebrate. Classically, diversity has been attributed to cells sensing their position with respect to external morphogen gradients. However, an alternative is that diversity arises in part from cooption of fluctuations in the gene regulatory network. Here we find ESCs exhibit intrinsic heterogeneity in the absence of external gradients by forming interconverting cell states. States vary in developmental gene expression programs and display distinct activity of microRNAs (miRNAs). Notably, miRNAs act on neighborhoods of pluripotency genes to increase variation of target genes and cell states. Loss of miRNAs that vary across states reduces target variation and delays state transitions, suggesting variable miRNAs organize and propagate variation to promote state transitions. Together these findings provide insight into how a gene regulatory network can coopt variation intrinsic to cell systems to form robust gene expression states. Interactions between intrinsic heterogeneity and environmental signals may help achieve developmental outcomes.

BK polyomavirus diversity-Why viral variation matters

BK polyomavirus (BKPyV or BKV) is a non-enveloped, circular double-stranded DNA virus that may exceed 80% seroprevalence in adults. BKV infection typically occurs during childhood, and the majority of adults are latently infected. While BKV infection is rarely associated with clinical disease in most individuals, in immunosuppressed individuals, reactivation may cause kidney (BK-associated nephropathy) or bladder (hemorrhagic cystitis and ureteral stenosis) injury. No antiviral therapies have been approved for the treatment of BKV infection. Reducing immunosuppression is the most effective therapy, although this is not feasible in many patients. Thus, a robust understanding of viral pathogenesis and viral diversity remains important for the development of future therapeutic strategies. Studies of BKV diversity are quite sparse compared to other common viral infections; thus, much of our understanding of BVK variability and evolution relies heavily analogous studies of other viruses such as HIV or viral hepatitis. We provide a comprehensive review of BKV diversity at the population and individual level with careful consideration of how viral variability may impact viral replication, pathogenesis, tropism, and protein function. We also discuss a number of outstanding questions related to BK virus diversity that should be explored rigorously in future studies.