Global patterns of human-wildlife spatial associations and implications for differentiating conservation strategies

Understanding the global patterns of human and wildlife spatial associations is essential for pragmatic conservation implementation, yet analytical foundations and indicator-based assessments that would further this understanding are lacking. We integrated the global distributions of 30,664 terrestrial vertebrates and human pressures to map human-nature index (HNI) categories that indicate the extent and intensity of human-wildlife interactions. Along the 2 dimensions of biodiversity and human activity, the HNI allowed placement of terrestrial areas worldwide in one of 4 HNI categories: anthropic (human-dominated areas), wildlife-dominated (little human influence and rich in wildlife), co-occurring (substantial presence of humans and wildlife), and harsh-environment (limited presence of humans and wildlife) areas. The HNI varied considerably among taxonomic groups, and the leading driver of HNI was global climate patterns. Co-occurring regions were the most prevalent (35.9%), and wildlife-dominated and anthropic regions encompassed 26.45% and 6.50% of land area, respectively. Our results highlight the necessity for customizing conservation strategies to regions based on human-wildlife spatial associations and the distribution of existing protected area networks. Human activity and biodiversity should be integrated for complementary strategies to support conservation toward ambitious and pragmatic 30×30 goals.

Study of association between corneal shape parameters and axial length elongation during orthokeratology using image-pro plus software

BACKGROUND

The aim was to validate the correlation between corneal shape parameters and axial length growth (ALG) during orthokeratology using Image-Pro Plus (IPP) 6.0 software.

METHODS

This retrospective study used medical records of myopic children aged 8-13 years (n = 104) undergoing orthokeratology. Their corneal topography and axial length were measured at baseline and subsequent follow-ups after lens wear. Corneal shape parameters, including the treatment zone (TZ) area, TZ diameter, TZ fractal dimension, TZ radius ratio, eccentric distance, pupil area, and pupillary peripheral steepened zone(PSZ) area, were measured using IPP software. The impact of corneal shape parameters at 3 months post-orthokeratology visit on 1.5-year ALG was evaluated using multivariate linear regression analysis.

RESULTS

ALG exhibited significant associations with age, TZ area, TZ diameter, TZ fractal dimension, and eccentric distance on univariate linear regression analysis. Multivariate regression analysis identified age, TZ area, and eccentric distance as significantly correlated with ALG (all P < 0.01), with eccentric distance showing the strongest correlation (β = -0.370). The regressive equation was y = 1.870 - 0.235a + 0.276b - 0.370c, where y represents ALG, a represents age, b represents TZ area, and c represents eccentric distance; R2 = 0.27). No significant relationships were observed between the TZ radius ratio, pupillary PSZ area, and ALG.

CONCLUSIONS

IPP software proves effective in capturing precise corneal shape parameters after orthokeratology. Eccentric distance, rather than age or the TZ area, significantly influences ALG retardation.

Genetics and Evolution of Bird Migration

Bird migration has long been a subject of fascination for humankind and is a behavior that is both intricate and multifaceted. In recent years, advances in technology, particularly in the fields of genomics and animal tracking, have enabled significant progress in our understanding of this phenomenon. In this review, we provide an overview of the latest advancements in the genetics of bird migration, with a particular focus on genomics, and examine various factors that contribute to the evolution of this behavior, including climate change. Integration of research from the fields of genomics, ecology, and evolution can enhance our comprehension of the complex mechanisms involved in bird migration and inform conservation efforts in a rapidly changing world.

Development of LOX-1 Antibody Modified Immuno-liposomes as Drug Carriers to Macrophages in Atherosclerotic Lesions

We developed a drug delivery system for atherosclerotic lesions using immuno-liposomes. We focused on enhancing the delivery efficiency of the liposomes to macrophages in atherosclerotic lesions by antibody modification of lectinlike oxidized low-density lipoproteins (LDL) receptor 1 (LOX-1). The cellular accumulation of the liposomes in foam cells induced by oxidized LDL (oxLDL) in Raw264 mouse macrophages was evaluated. The cellular accumulation of LOX-1 antibody modified liposomes in oxLDL-induced foam cells and untreated Raw264 cells was significantly higher compared with that of unmodified liposomes. The liposomes were also administered intravenously to Apoeshl mice as an atherosclerosis model. Frozen sections were prepared from the mouse aortas and observed by confocal laser microscopy. The distribution of LOX-1 antibody modified liposomes in the atherosclerotic regions of Apoeshl mice was significantly greater compared with that of unmodified liposomes. The results suggest that LOX-1 antibody modified liposomes can target foam cells in atherosclerotic lesions, providing a potential route for delivering various drugs with pharmacological effects or detecting atherosclerotic foci for the diagnosis of atherosclerosis.

Whole-genome survey reveals extensive variation in genetic diversity and inbreeding levels among peregrine falcon subspecies

In efforts to prevent extinction, resource managers are often tasked with increasing genetic diversity in a population of concern to prevent inbreeding depression or improve adaptive potential in a changing environment. The assumption that all small populations require measures to increase their genetic diversity may be unwarranted, and limited resources for conservation may be better utilized elsewhere. We test this assumption in a case study focused on the peregrine falcon (Falco peregrinus), a cosmopolitan circumpolar species with 19 named subspecies. We used whole-genome resequencing to generate over two million single nucleotide polymorphisms (SNPs) from multiple individuals of all peregrine falcon subspecies. Our analyses revealed extensive variation among subspecies, with many island-restricted and nonmigratory populations possessing lower overall genomic diversity, elevated inbreeding coefficients (F _ROH)-among the highest reported, and extensive runs of homozygosity (ROH) compared to mainland and migratory populations. Similarly, the majority of subspecies that are either nonmigratory or restricted to islands show a much longer history of low effective population size (N _e). While mutational load analyses indicated an increased proportion of homozygous-derived deleterious variants (i.e., drift load) among nonmigrant and island populations compared to those that are migrant or reside on the mainland, no significant differences in the proportion of heterozygous deleterious variants (i.e., inbreeding load) was observed. Our results provide evidence that high levels of inbreeding may not be an existential threat for some populations or taxa. Additional factors such as the timing and severity of population declines are important to consider in management decisions about extinction potential.

SARS-CoV-2 RNAs are processed into 22-nt vsRNAs in Vero cells

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the global pandemic, resulting in great fatalities around the world. Although the antiviral roles of RNA interference (RNAi) have been well studied in plants, nematodes and insects, the antiviral roles of RNAi in mammalians are still debating as RNAi effect is suspected to be suppressed by interferon (IFN) signaling pathways in most cell types. To determine the role of RNAi in mammalian resistance to SARS-CoV-2, we studied the profiling of host small RNAs and SARS-CoV-2 virus-derived small RNAs (vsRNAs) in the early infection stages of Vero cells, an IFN-deficient cell line. We found that host microRNAs (miRNAs) were dysregulated upon SARS-CoV-2 infection, resulting in downregulation of microRNAs playing antiviral functions and upregulation of microRNAs facilitating viral proliferations. Moreover, vsRNA peaked at 22 nt at negative strand but not the positive strand of SARS-CoV-2 and formed successive Dicer-spliced pattern at both strands. Similar characteristics of vsRNAs were observed in IFN-deficient cell lines infected with Sindbis and Zika viruses. Together, these findings indicate that host cell may deploy RNAi pathway to combat SARS-CoV-2 infection in IFN-deficient cells, informing the alternative antiviral strategies to be developed for patients or tissues with IFN deficiency.

Arctic introgression and chromatin regulation facilitated rapid Qinghai-Tibet Plateau colonization by an avian predator

The Qinghai-Tibet Plateau (QTP), possesses a climate as cold as that of the Arctic, and also presents uniquely low oxygen concentrations and intense ultraviolet (UV) radiation. QTP animals have adapted to these extreme conditions, but whether they obtained genetic variations from the Arctic during cold adaptation, and how genomic mutations in non-coding regions regulate gene expression under hypoxia and intense UV environment, remain largely unknown. Here, we assemble a high-quality saker falcon genome and resequence populations across Eurasia. We identify female-biased hybridization with Arctic gyrfalcons in the last glacial maximum, that endowed eastern sakers with alleles conveying larger body size and changes in fat metabolism, predisposing their QTP cold adaptation. We discover that QTP hypoxia and UV adaptations mainly involve independent changes in non-coding genomic variants. Our study highlights key roles of gene flow from Arctic relatives during QTP hypothermia adaptation, and cis-regulatory elements during hypoxic response and UV protection.

Systematic Analysis of Mobile Genetic Elements Mediating β-Lactamase Gene Amplification in Noncarbapenemase-Producing Carbapenem-Resistant Enterobacterales Bloodstream Infections

Noncarbapenemase-producing carbapenem-resistant Enterobacterales (non-CP-CRE) are increasingly recognized as important contributors to prevalent carbapenem-resistant Enterobacterales (CRE) infections. However, there is limited understanding of mechanisms underlying non-CP-CRE causing invasive disease. Long- and short-read whole-genome sequencing was used to elucidate carbapenem nonsusceptibility determinants in Enterobacterales bloodstream isolates at MD Anderson Cancer Center in Houston, Texas. We investigated carbapenem nonsusceptible Enterobacterales (CNSE) mechanisms (i.e., isolates with carbapenem intermediate resistance phenotypes or greater) through a combination of phylogenetic analysis, antimicrobial resistance gene detection/copy number quantification, porin assessment, and mobile genetic element (MGE) characterization. Most CNSE isolates sequenced were non-CP-CRE (41/79; 51.9%), whereas 25.3% (20/79) were Enterobacterales with intermediate susceptibility to carbapenems (CIE), and 22.8% (18/79) were carbapenemase-producing Enterobacterales (CPE). Statistically significant copy number variants (CNVs) of extended-spectrum β-lactamase (ESBL) genes (Wilcoxon Test; P-value < 0.001) were present in both non-CP-CR E. coli (median CNV = 2.6×; n = 17) and K. pneumoniae (median CNV = 3.2×, n = 17). All non-CP-CR E. coli and K. pneumoniae had predicted reduced expression of at least one outer membrane porin gene (i.e., ompC/ompF or ompK36/ompK35). Completely resolved CNSE genomes revealed that IS26 and ISEcp1 structures harboring blaCTX-M variants along with other antimicrobial resistance elements were associated with gene amplification, occurring in mostly IncFIB/IncFII plasmid contexts. MGE-mediated β-lactamase gene amplifications resulted in either tandem arrays, primarily mediated by IS26 translocatable units, or segmental duplication, typically due to ISEcp1 transposition units. Non-CP-CRE strains were the most common cause of CRE bacteremia with carbapenem nonsusceptibility driven by concurrent porin loss and MGE-mediated amplification of blaCTX-M genes. IMPORTANCE Carbapenem-resistant Enterobacterales (CRE) are considered urgent antimicrobial resistance (AMR) threats. The vast majority of CRE research has focused on carbapenemase-producing Enterobacterales (CPE) even though noncarbapenemase-producing CRE (non-CP-CRE) comprise 50% or more of isolates in some surveillance studies. Thus, carbapenem resistance mechanisms in non-CP-CRE remain poorly characterized. To address this problem, we applied a combination of short- and long-read sequencing technologies to a cohort of CRE bacteremia isolates and used these data to unravel complex mobile genetic element structures mediating β-lactamase gene amplification. By generating complete genomes of 65 carbapenem nonsusceptible Enterobacterales (CNSE) covering a genetically diverse array of isolates, our findings both generate novel insights into how non-CP-CRE overcome carbapenem treatments and provide researchers scaffolds for characterization of their own non-CP-CRE isolates. Improved recognition of mechanisms driving development of non-CP-CRE could assist with design and implementation of future strategies to mitigate the impact of these increasingly recognized AMR pathogens.

[Clinical and StAR genetic characteristics of 33 children with congenital lipoid adrenal hyperplasia]

Objective: To analyze the clinical and genetic characteristics of 33 children with congenital lipoid adrenal hyperplasia (CLAH) caused by StAR gene defects. Methods: The clinical, biochemical, genetic, and follow-up (until December 2021) data of 33 children diagnosed with CLAH from 2006 to 2021 were retrospectively analyzed in Xinhua Hospital, Shanghai Jiao Tong University School of Medicine. Results: Of the 33 children with CLAH, 17 had a karyotype of 46, XX and 16 had a karyotype of 46, XY; 31 were female and 2 were male by social gender. Classic type and non-classic type were found in 30 and 3 children respectively. The age at diagnosis was 9.0 (3.0, 34.5) months. All the 30 cases with classic CLAH presented within the first year of life with skin hyperpigmentation (28 cases, 93%), vomiting and(or) diarrhea (19 cases, 63%), no increase in body weight (8 cases, 27%), elevated adrenocorticotropic hormone levels (21cases (70%)>275 pmol/L), decreased cortisol levels (47 (31,126) nmol/L), hyponatremia ((126±13) mmol/L), hyperkalemia ((5.7±1.1) mmol/L), and normal 17α-hydroxyprogesterone levels (30 cases, 100%). All these with classic CLAH exhibited female external genitalia. Three children with non-classic CLAH (including 2 cases of 46, XY and 1 case of 46, XX) also showed signs and symptoms of adrenal insufficiency, but 2 of them had an age of onset later than 1 year of age, including 1 case of 46, XY with male external genitalia and 1 case of 46, XX with female external genitalia. The other 46, XY patient with non-classic CLAH presented with adrenal insufficiency at 2 months of age, showing micropenis and hypospadias. In the 17 females with 46, XX, 4 older than 10 years of age showed spontaneous pubertal development. A total of 25 StAR gene pathogenic variants were identified in 33 patients, with p.Q258* (18/66, 27%), p.K236Tfs*47 (8/66, 12%) and p.Q77* (6/66, 9%) being the common variantion. Six novel variants were found, including c.358T>G, c.713_714del, c.125del, c.745-1G>A, c.179-2A>C, and exon 1 deletion. Conclusions: Patients with classic CLAH typically present with signs and symptoms of primary adrenal insufficiency in the early infancy period and female external genitalia. p.Q258*, p.K236Tfs*47 and p.Q77* are common variants in CLAH patients.

[Disease spectrum analysis of children with inherited metabolic diseases detected by gas chromatography-mass spectrometry of urinary organic acids]

Objective: To investigate the spectrum of amino acid, organic acid, and fatty acid oxidative metabolic diseases in children diagnosed by detecting urinary organic acid levels using gas chromatography-mass spectrometry. Methods: From January 2005 to December 2021, clinical data of 2 461 children diagnosed with inherited metabolic diseases (IMD) by gas chromatography-mass spectrometry, in combination with tandem mass spectrometry and genetic testing in Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine were retrospectively analyzed. Results: Among 2 461 children, 1 446 were male and 1 051 were female. A total of 32 types of IMD were detected among 2 461 patients, which included 10 amino acid disorders in 662 cases (26.9%), 6 common diseases were hyperphenylalaninemia, citrin deficiency, ornithine carbamoyltransferase deficiency, maple syrup urine disease, alkaptonuria, and tyrosinemia-I, 17 types of organic acidemias in 1 683 cases (68.4%), 6 common diseases were methylmalonic acidemia, propionic acidemia, valeric acidemia-type Ⅰ, isovaleric acidemia, 3-methylcrotonyl-CoA carboxylase deficiency and multiple carboxylase deficiency and 5 fatty acid β oxidative defects in 116 cases (4.7%), 2 common diseases were multiple acyl-CoA dehydrogenase deficiency and short-chain acyl-CoA dehydrogenase deficiency). Conclusion: Among the diseases diagnosed by analyzing urinary organic acid profiling with gas chromatography-mass spectrometry, the most common are organic acidemias, followed by amino acid disorders and fatty acid oxidation defects.

Evolutionary conservation genomics reveals recent speciation and local adaptation in threatened takins

Incorrect species delimitation will lead to inappropriate conservation decisions, especially for threatened species. The takin (Budorcas taxicolor) is a large artiodactyl endemic to the Himalayan–Hengduan–Qinling Mountains and is well known for its threatened status and peculiar appearance. However, the speciation, intraspecies taxonomy, evolutionary history, and adaptive evolution of this species still remain unclear, which greatly hampers its scientific conservation. Here, we de novo assembled a high-quality chromosome-level genome of takin and resequenced the genomes of 75 wild takins. Phylogenomics revealed that takin was positioned at the root of Caprinae. Population genomics based on the autosome, X chromosome, and Y chromosome SNPs and mitochondrial genomes consistently revealed the existence of two phylogenetic species and recent speciation in takins: the Himalayan takin (B. taxicolor) and the Chinese takin (B. tibetana), with the support of morphological evidence. Two genetically divergent subspecies were identified in both takin species, rejecting three previously proposed taxonomical viewpoints. Furthermore, their distribution boundaries were determined, suggesting that large rivers play important roles in shaping the genetic partition. Compared with the other subspecies, the Qinling subspecies presented the lowest genomic diversity, higher linkage disequilibrium, inbreeding, and genetic load, thus is in urgent need of genetic management and protection. Moreover, coat color gene (PMEL) variation may be responsible for the adaptive coat color difference between the two species following Gloger’s rule. Our findings provide novel insights into the recent speciation, local adaptation, scientific conservation of takins, and biogeography of the Himalaya–Hengduan biodiversity hotspot.

Rapid Spread of Severe Fever with Thrombocytopenia Syndrome Virus by Parthenogenetic Asian Longhorned Ticks

Severe fever with thrombocytopenia syndrome virus (SFTSV) is spreading rapidly in Asia. This virus is transmitted by the Asian longhorned tick (Haemaphysalis longicornis), which has parthenogenetically and sexually reproducing populations. Parthenogenetic populations were found in ≥15 provinces in China and strongly correlated with the distribution of severe fever with thrombocytopenia syndrome cases. However, distribution of these cases was poorly correlated with the distribution of populations of bisexual ticks. Phylogeographic analysis suggested that the parthenogenetic population spread much faster than bisexual population because colonization is independent of sexual reproduction. A higher proportion of parthenogenetic ticks was collected from migratory birds captured at an SFTSV-endemic area, implicating the contribution to the long-range movement of these ticks in China. The SFTSV susceptibility of parthenogenetic females was similar to that of bisexual females under laboratory conditions. These results suggest that parthenogenetic Asian longhorned ticks, probably transported by migratory birds, play a major role in the rapid spread of SFTSV.

RNA-combine: a toolkit for comprehensive analyses on transcriptome data from different sequencing platforms

Background

Understanding the transcriptome has become an essential step towards the full interpretation of the biological function of a cell, a tissue or even an organ. Many tools are available for either processing, analysing transcriptome data, or visualizing analysis results. However, most existing tools are limited to data from a single sequencing platform and only several of them could handle more than one analysis module, which are far from enough to meet the requirements of users, especially those without advanced programming skills. Hence, we still lack an open-source toolkit that enables both bioinformatician and non-bioinformatician users to process and analyze the large transcriptome data from different sequencing platforms and visualize the results.

Results

We present a Linux-based toolkit, RNA-combine, to automatically perform the quality assessment, downstream analysis of the transcriptome data generated from different sequencing platforms, including bulk RNA-seq (Illumina platform), single cell RNA-seq (10x Genomics) and Iso-Seq (PacBio) and visualization of the results. Besides, this toolkit is implemented with at least 10 analysis modules more than other toolkits examined in this study. Source codes of RNA-combine are available on GitHub: https://github.com/dongxuemin666/RNA-combine.

Conclusion

Our results suggest that RNA-combine is a reliable tool for transcriptome data processing and result interpretation for both bioinformaticians and non-bioinformaticians.

[HBx promotes ubiquitination and degradation of ZO1 and increases the migration and invasion of liver cancer cells]

Objective: To study the effect of hepatitis B virus X protein (HBx) expression level on migration and invasion of zonula occludens protein-1 (ZO-1) in HepG2 liver cancer cells. Methods: Liver cancer cells were transfected with HBV full gene plasmid (pcDNA3.1-HBV1. 1 or pcDNA3.1-HBV1.3), empty plasmid (pcDNA3.1) and HBV-encoded protein plasmids (pHBc, pHBs, pHBp and pHBx), respectively. Western blot and RT-PCR were used to detect ZO1 protein and mRNA levels. Immunoprecipitation was used to detect transfected pHBx. Western blot was used to detect ZO1 ubiquitination levels. Transwell chambers were used to assess cell migration and invasion. Cell proliferation and lactate dehydrogenase assay was used to detect siRNA transfecting targeting ZO1. Flow cytometry was used to detect cell apoptosis and cycle. The data was compared between two and multiple groups by using an independent sample t-test and one-way analysis of variance. Results: Compared with the empty plasmid, ZO1 protein level in HepG2 cells after transiently transfected with pHBV1.1 and pHBV1.3 was decreased by 42.99% ± 6.8% and 55.0% 5 ± 4.56%, respectively, and their mRNA levels did not change significantly. ZO1 protein level in Huh7 cells was decreased by 17.46% ± 4.94% and 47.53% ± 3.38%, respectively. ZO1 protein level after transfection with pHBx was decreased by 47.02% ± 3.4%, while the ZO1 protein level after transfection with pHBc, pHBs and pHBp did not change significantly. ZO1 mRNA level was unaffected with pHBx transfection. ZO1 ubiquitin level and cell migration and invasion ability in HepG2 cells was significantly increased with transfected pHBx. HepG2 cells proliferation, apoptosis and cycle after transfection with ZO1-targeted siRNA did not change significantly, but the migration and invasion ability were significantly increased. Conclusion: HBx can increase the migration and invasion of liver cancer cells by promoting the ubiquitination and degradation of ZO1 protein level.

[Analysis of six children with 3-methylglutaconic aciduria]

Objective: To explore the clinical characteristics, genotypes and long-term outcomes of individuals with 3-methylglutaconic aciduria. Methods: The clinical features, biochemical data, genetic test results and treatment outcomes of six children with 3-methylglutaconic aciduria admitted to the Department of Endocrinology, Genetics and Metabolism, Xinhua Hospital from February 2017 to February 2019 were retrospectively analyzed and the Gesell developmental diagnosis schedule was performed to evaluate the development of four patients. Results: Among 6 children with 3-methylglutaconic aciduria 2 were males and 4 were females.Four cases had 3-methylglutaconic aciduria type Ⅰ and 2 cases had 3-methylglutaconic aciduria with deafness,encephalopathy, and Leigh-like syndrome. Five of 6 patients were detected by newborn screening among whom 4 remained asymptomatic, and only one had a postmortem diagnosis. Among them, 4 patients remained asymptomatic, while two presented with clinical symptoms such as jaundice and dyspnea and the age of disease onset was 1 and 2 days respectively. The concentration of 3-methylglutaconic acid in urine of all affected individuals was between 22.38 and 77.09 mmol/molCr, which was above the normal value. Genetic tests were performed for all patients. Eleven variants were identified in 2 genes, of which 10 variants were novel and only c.442C>T p.(R148X) has been previously reported; Seven variants (c.656-2delA, EX5-EX6 Del, c.942+3A>G, c.373C>T p.(R125W), c.895-3C>G, c.667C>T p.(R223X) and c.894+5G>A) were in AUH gene. The others (c.548G>A p.(R138Q), c.442C>T p.(R148X), c.1339C>T p.(R447X) and c.973dupA p.(M325Nfs*5) were in SERAC1 gene. After being treated with leucine diet restriction and L-carnitine, 4 patients with AUH gene variation who were from asymptomatic phase developed normally, whereas those 2 patients with SERAC1 gene variation had a poor prognosis. During the follow-up, 2 patients exhibited varying degrees of psychomotor retardation, the rest had normal course of development. Conclusions: There are significant clinical heterogeneities among individuals with 3-methylglutaconic aciduria. The most common pathogenic variants are splicing variations, followed by nonsense, missense and frameshift mutations. Leucine-free diet and oral L-carnitine therapy are effective for some patients. Newborn screening is essential for early diagnosis and improvement of prognosis.

Enrichment of Autotrophic Denitrifiers From Anaerobic Sludge Using Sulfurous Electron Donors

This study compared the rates and microbial community development in batch bioassays on autotrophic denitrification using elemental sulfur (S0), pyrite (FeS2), thiosulfate (S2O3 2-), and sulfide (S2-) as electron donor. The performance of two inocula was compared: digested sludge (DS) from a wastewater treatment plant of a dairy industry and anaerobic granular sludge (GS) from a UASB reactor treating dairy wastewater. All electron donors supported the development of a microbial community with predominance of autotrophic denitrifiers during the enrichments, except for sulfide. For the first time, pyrite revealed to be a suitable substrate for the growth of autotrophic denitrifiers developing a microbial community with predominance of the genera Thiobacillus, Thioprofundum, and Ignavibacterium. Thiosulfate gave the highest denitrification rates removing 10.94 mM NO3 - day-1 and 8.98 mM NO3 - day-1 by DS and GS, respectively. This was 1.5 and 6 times faster than elemental sulfur and pyrite, respectively. Despite the highest denitrification rates observed in thiosulfate-fed enrichments, an evaluation of the most relevant parameters for a technological application revealed elemental sulfur as the best electron donor for autotrophic denitrification with a total cost of 0.38 € per m3 of wastewater treated.

[Effects of pressure steam sterilization times on the accuracy of the digital intraoral scanning data]

Objective: To provide a scientific basis for the standardized operation of clinical disinfection by comparing and analyzing the influence of disinfection times on the accuracy of digital intraoral scanning. Methods: The author prepared 10 brand-new intraoral scanning heads (Trios, 3Shape, Denmark), scan the same plaster standard dentition model after 1, 20, 40, and 60 times of pressure steam sterilization, and obtained the data of four groups of experimental groups A, B, C, D, and scan the model 5 times repeatedly after each disinfection cycle of each scanning head. A model scanner (D2000, 3Shape, Denmark) was used to scan the standard dentition model, and the scan results were used as the control group data. Vernier calipers and measurement software were used to measure the arch length (the distance between the mesial cheek tips of the first molars on both sides of the maxillary) and the front and back length (the distance from the tongue protrusion of the right incisor to the buccal tip of the first molar on the right of the upper jaw) of the plaster model and the data of the 4 experimental groups. The line distance results of the 4 groups of experimental groups were compared for statistical analysis, and the trueness and precision values of the 4 groups of experimental groups were compared for statistical analysis. Results: The length of the arch across the 4 experimental groups increased with the increase in the number of disinfection (P<0.05), and there were statistical differences compared with the measurement results of the plaster model (P<0.05); the differences in the length of the dental arch were not statistically significant (P>0.05). The treness of the 4 experimental groups is statistically significant (P<0.05), and the trueness was from high to low in order of group A [(114.85±3.75) μm], group B [(124.65±3.85) μm], group C [(131.45±3.04) μm] and group D [(144.64±3.34) μm]; the precision of the 4 experimental groups was not statistically significant (P>0.05). Conclusions: The number of times of pressure steam sterilization can affect the accuracy of the scanning results of the digital intraoral scanner, and with the increase of the number of sterilizations, the error of the scanning results also tends to increase. The number of sterilizations has no effect on the repeatability of the digital scanning results. The increase in the number of times of pressure steam sterilization affects the accross of the arch but has no effect on the length of the dental arch, and the range of change of the length of the arch is within the clinically acceptable range. After 60 times of pressure steam sterilization, the accuracy of digital scan data can still meet clinical needs.

Climate-driven flyway changes and memory-based long-distance migration

Millions of migratory birds occupy seasonally favourable breeding grounds in the Arctic¹, but we know little about the formation, maintenance and future of the migration routes of Arctic birds and the genetic determinants of migratory distance. Here we established a continental-scale migration system that used satellite tracking to follow 56 peregrine falcons (Falco peregrinus) from 6 populations that breed in the Eurasian Arctic, and resequenced 35 genomes from 4 of these populations. The breeding populations used five migration routes across Eurasia, which were probably formed by longitudinal and latitudinal shifts in their breeding grounds during the transition from the Last Glacial Maximum to the Holocene epoch. Contemporary environmental divergence between the routes appears to maintain their distinctiveness. We found that the gene ADCY8 is associated with population-level differences in migratory distance. We investigated the regulatory mechanism of this gene, and found that long-term memory was the most likely selective agent for divergence in ADCY8 among the peregrine populations. Global warming is predicted to influence migration strategies and diminish the breeding ranges of peregrine populations of the Eurasian Arctic. Harnessing ecological interactions and evolutionary processes to study climate-driven changes in migration can facilitate the conservation of migratory birds.

Spatial patterns and conservation of genetic and phylogenetic diversity of wildlife in China

Genetic diversity and phylogenetic diversity reflect the evolutionary potential and history of species, respectively. However, the levels and spatial patterns of genetic and phylogenetic diversity of wildlife at the regional scale have largely remained unclear. Here, we performed meta-analyses of genetic diversity in Chinese terrestrial vertebrates based on three genetic markers and investigated their phylogenetic diversity based on a dated phylogenetic tree of 2461 species. We detected strong positive spatial correlations among mitochondrial DNA-based genetic diversity, phylogenetic diversity, and species richness. Moreover, the terrestrial vertebrates harbored higher genetic and phylogenetic diversity in South China and Southwest China than in other regions. Last, climatic factors (precipitation and temperature) had significant positive effects while altitude and human population density had significant negative impacts on levels of mitochondrial DNA-based genetic diversity in most cases. Our findings will help guide national-level genetic diversity conservation plans and a post-2020 biodiversity conservation framework.

Deeply digging the interaction effect in multiple linear regressions using a fractional-power interaction term

In multiple regression Y ~ β₀ + β₁X₁ + β₂X₂ + β₃X₁ X₂ + ɛ., the interaction term is quantified as the product of X₁ and X₂. We developed fractional-power interaction regression (FPIR), using βX₁^M X₂^N as the interaction term. The rationale of FPIR is that the slopes of Y-X₁ regression along the X₂ gradient are modeled using the nonlinear function (Slope = β₁ + β₃MX₁^M-1 X₂^N), instead of the linear function (Slope = β₁ + β₃X₂) that regular regressions normally implement. The ranges of M and N are from -56 to 56 with 550 candidate values, respectively. We applied FPIR using a well-studied dataset, nest sites of the crested ibis (Nipponia nippon).We further tested FPIR by other 4692 regression models. FPIRs have lower AIC values (-302 ± 5003.5) than regular regressions (-168.4 ± 4561.6), and the effect size of AIC values between FPIR and regular regression is 0.07 (95% CI: 0.04–0.10). We also compared FPIR with complex models such as polynomial regression, generalized additive model, and random forest. FPIR is flexible and interpretable, using a minimum number of degrees of freedom to maximize variance explained. We have provided a new R package, interactionFPIR, to estimate the values of M and N, and suggest using FPIR whenever the interaction term is likely to be significant.

• Introduced fractional-power interaction regression (FPIR) as Y ~ β₀ + β₁X₁ + β₂X₂ + β₃X₁^M X₂^N + ɛ to replace the current regression model Y ~ β₀ + β₁X₁ + β₂X₂ + β₃X₁ X₂ + ɛ;

• Clarified the rationale of FPIR, and compared it with regular regression model, polynomial regression, generalized additive model, and random forest using regression models for 4692 species;

• Provided an R package, interactionFPIR, to calculate the values of M and N, and other model parameters.

[Postinflammatroy pulmonary fibrosis of COVID-19: the current status and perspective]

The novel coronavirus pneumonia (COVID-19) has been well controlled in China. Most of the COVID-19 patients were having postinflammatory pulmonary fibrosis (PPF) on the follow-up CT scan when discharged, and complaining about exertional dyspnea of different levels, presenting with an UIP (usual interstitial pneumonia) pattern or NSIP (non-specific interstitial pneumonia) pattern on the CT scans. Will the PPF get improved or stay stable, or progress? Such questions could only be answered by follow-up and monitoring of the pulmonary function. At the same time, we should learn from the lessons on pulmonary function loss of the SARS patients and MERS patients, some of whom had persistent impaired lung function after discharge. Pirfenidone and Nintedanib had been approved for the treatment of idiopathic pulmonary fibrosis(IPF), showing effectiveness on non-IPF pulmonary fibrosis as well. However, there are no studies about the application on PPF resulting from viral pneumonia. Given the follow-up status of SARS patients and MERS patients, and the PPF of COVID-19 patients, we should be careful about the discharged patients with a close follow-up, and further studies on PPF of COVID-19 are needed.

Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca

BACKGROUND

Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and alpaca remain poorly understood. Here we report reference genomes for the llama, and for the guanaco and vicuña (their putative wild progenitors), compare these with the published alpaca genome, and resequence seven individuals of all four species to better understand domestication and introgression between the llama and alpaca.

RESULTS

Phylogenomic analysis confirms that the llama was domesticated from the guanaco and the alpaca from the vicuña. Introgression was much higher in the alpaca genome (36%) than the llama (5%) and could be dated close to the time of the Spanish conquest, approximately 500 years ago. Introgression patterns are at their most variable on the X-chromosome of the alpaca, featuring 53 genes known to have deleterious X-linked phenotypes in humans. Strong genome-wide introgression signatures include olfactory receptor complexes into both species, hypertension resistance into alpaca, and fleece/fiber traits into llama. Genomic signatures of domestication in the llama include male reproductive traits, while in alpaca feature fleece characteristics, olfaction-related and hypoxia adaptation traits. Expression analysis of the introgressed region that is syntenic to human HSA4q21, a gene cluster previously associated with hypertension in humans under hypoxic conditions, shows a previously undocumented role for PRDM8 downregulation as a potential transcriptional regulation mechanism, analogous to that previously reported at high altitude for hypoxia-inducible factor 1α.

CONCLUSIONS

The unprecedented introgression signatures within both domestic camelid genomes may reflect post-conquest changes in agriculture and the breakdown of traditional management practices.

[Pharmacotherapeutics for the new coronavirus pneumonia]

The new coronavirus pneumonia (NCP), also named as COVID-19 by WHO on Feb 11 2020, is now causing a severe public health emergency in China since. The number of diagnosed cases is more than 40,000 until the submission of this manuscript. Coronavirus has caused several epidemic situations world widely, but the present contagious disease caused by 2019 new coronavirus is unprecedentedly fulminating. The published cohorts of 2019 new coronavirus (n-Cov) are single-center studies, or retrospective studies. We here share the therapeutic experiences of NCP treatment with literature review. Combination of Ribavirin and interferon-α is recommended by the 5(th) edition National Health Commission's Regimen (Revised Edition) because of the effect on Middle East respiratory syndrome (MERS), and the effectiveness of Lopinavir/Ritonavir and Remdisivir needs to be confirmed by randomized controlled trial (RCT), given the situation of no specific antivirus drug on NCP is unavailable. Systemic glucocorticosteroid is recommended as a short term use (1~2 mg·kg(-1)·d(-1), 3~5 d) by the 5(th) edition National Health Commission's Regimen (Revised Edition) yet RCTs are expected to confirm the effectiveness. Inappropriate application of antibiotics should be avoided, especially the combination of broad-spectrum antibiotics, for the NCP is not often complicated with bacterial infection.

[Pharmacotherapeutics for the New Coronavirus Pneumonia]

The New Coronavirus Pneumonia (NCP, also named as COVID-19 by WHO on Feb 11 2020, is now causing a severe public health emergency in China since. The number of diagnosed cases is more than 40,000 until the submission of this manuscript. Coronavirus has caused several epidemic situations world widely, but the present contagious disease caused by 2019 new Coronavirus is unprecedentedly fulminating. The published cohorts of 2019 new Coronavirus (n-Cov) are single-center studies, or retrospective studies. We here share the therapeutic experiences of NCP treatment with literature review. Combination of Ribavirin and Interferon-α is recommended by the 5(th) edition National Health Commission's Regimen (Revised Edition) because of the effect on MERS (Middle East Respiratory Syndrome), and the effectiveness of Lopinavir/Ritonavir and Remdisivir needs to be confirmed by randomized controlled trial (RCT), given the situation of no specific antivirus drug on NCP is unavailable. Systemic glucocorticosteroid is recommended as a short term use (1~2 mg.kg(-1).d(-1), 3~5d ) by the 5(th) edition National Health Commission's Regimen (Revised Edition) yet RCTs are expected to confirm the effectiveness. Inappropriate application of antibiotics should be avoided, especially the combination of broad-spectrum antibiotics, for the NCP is not often complicated with bacterial infection.

[Related factors on skip metastasis of neck lymph node in papillary thyroid carcinoma]

Objective: To investigate the correlation between skip metastasis of neck lymph node and clinicopathological features in papillary thyroid carcinoma. Methods: Totally 272 papillary thyroid carcinoma patients with lateral lymph node metastases who received surgical procedure at Department of Thyroid Surgery, the First Hospital of the Jilin University from January 2014 to June 2016 were analyzed retrospectively. There were 105 male and 167 female patients, aging from 16 to 73 years with a mean age of (42±8) years. There were 29 patients (10.7%) with skip metastasis. And then the correlation between skip metastasis of neck lymph node and clinicopathological features was analyzed by χ(2) test and multivariate Logistic regression test. Results: The rate of skip metastasis in all patients was 10.7% (29/272). By summarizing the distribution of the lateral lymph nodes about the patients with skip metastasis, 16 cases metastasized in single level (55.2%), meanwhile 6 in two levels (20.7%) and 7 in three levels (24.1%). Strong correlation between age, tumor location and skip metastasis was found using χ(2) test (χ(2) values were 14.056 and 21.362 respectively, both P values were 0.000). Age (>45 years) (OR=4.318, 95% CI: 1.767 to 10.552, P=0.001), microcarcinoma (OR=2.623, 95% CI: 1.013 to 6.795, P=0.047)and the tumor located in the upper of the thyroid (OR=11.982, 95% CI: 2.533 to 56.173, P=0.002) were risk factors to the skip metastasis through multivariable Logistic regression analysis. Conclusions: Age >45 years old, microcarcinoma or tumor located in the upper part of the thyroid gland was more likely present with skip metastasis. Skip metastases are often involved in the lateral multi-level. Therefore, confronted patients with one of these risk factors, the occurrence of skip metastasis should be awared when the lateral lymph node was large abnormally. Accordingly, it may be appropriate to extend the indications of fine needle aspiration for lateral lymph node in order to prevent missed diagnosis.

Integrated tool for microsatellite isolation and validation from the reference genome and their application in the study of breeding turnover in an endangered avian population

Accurate individual identification is required to estimate survival rates in avian populations. For endangered species, non-invasive methods of obtaining individual identification, such as using molted feathers as a source of DNA for microsatellite markers, are preferred because of less disturbance, easy sample preparation and high efficiency. With the availability of many avian genomes, a few pipelines isolating genome-wide microsatellites have been published, but it is still a challenge to isolate microsatellites from the reference genome efficiently. Here, we have developed an integrated tool comprising a bioinformatic pipeline and experimental procedures for microsatellite isolation and validation based on the reference genome. We have identified over 95 000 microsatellite loci and established a system comprising 10 highly polymorphic markers (PIC value: 0.49-0.93, mean: 0.79) for an endangered species, saker falcon (Falco cherrug). These markers (except 1) were successfully amplified in 126 molted feathers, exhibiting high amplification success rates (83.9-99.7%), high quality index (0.90-0.97) and low allelic dropout rates (1-9.5%). To further assess the efficiency of this marker system in a population study, we identified individual sakers using these molted feathers (adult) and 146 plucked feathers (offspring). The use of parent and offspring samples enabled us to infer the genotype of missing samples (N = 28), and all adult genotypes were used to ascertain that breeding turnover is a useful proxy for survival estimation in sakers. Our study presents a cost-effective tool for microsatellite isolation based on publicly available reference genomes and demonstrates the power of this tool in estimating key parameters of avian population dynamics.

The Value of Ecosystem Services from Giant Panda Reserves

Ecosystem services (the benefits to humans from ecosystems) are estimated globally at $125 trillion/year [1, 2]. Similar assessments at national and regional scales show how these services support our lives [3]. All valuations recognize the role of biodiversity, which continues to decrease around the world in maintaining these services [4, 5]. The giant panda epitomizes the flagship species [6]. Its unrivalled public appeal translates into support for conservation funding and policy, including a tax on foreign visitors to support its conservation [7]. The Chinese government has established a panda reserve system, which today numbers 67 reserves [8, 9]. The biodiversity of these reserves is among the highest in the temperate world [10], covering many of China's endemic species [11]. The panda is thus also an umbrella species [12]-protecting panda habitat also protects other species. Despite the benefits derived from pandas, some journalists have suggested that it would be best to let the panda go extinct. With the recent downlisting of the panda from Endangered to Vulnerable, it is clear that society's investment has started to pay off in terms of panda population recovery [13, 14]. Here, we estimate the value of ecosystem services of the panda and its reserves at between US$2.6 and US$6.9 billion/year in 2010. Protecting the panda as an umbrella species and the habitat that supports it yields roughly 10-27 times the cost of maintaining the current reserves, potentially further motivating expansion of the reserves and other investments in natural capital in China.

Transcription-Associated Mutation Promotes RNA Complexity in Highly Expressed Genes-A Major New Source of Selectable Variation

Alternatively spliced transcript isoforms are thought to play a critical role for functional diversity. However, the mechanism generating the enormous diversity of spliced transcript isoforms remains unknown, and its biological significance remains unclear. We analyzed transcriptomes in saker falcons, chickens, and mice to show that alternative splicing occurs more frequently, yielding more isoforms, in highly expressed genes. We focused on hemoglobin in the falcon, the most abundantly expressed genes in blood, finding that alternative splicing produces 10-fold more isoforms than expected from the number of splice junctions in the genome. These isoforms were produced mainly by alternative use of de novo splice sites generated by transcription-associated mutation (TAM), not by the RNA editing mechanism normally invoked. We found that high expression of globin genes increases mutation frequencies during transcription, especially on nontranscribed DNA strands. After DNA replication, transcribed strands inherit these somatic mutations, creating de novo splice sites, and generating multiple distinct isoforms in the cell clone. Bisulfate sequencing revealed that DNA methylation may counteract this process by suppressing TAM, suggesting DNA methylation can spatially regulate RNA complexity. RNA profiling showed that falcons living on the high Qinghai-Tibetan Plateau possess greater global gene expression levels and higher diversity of mean to high abundance isoforms (reads per kilobases per million mapped reads ≥18) than their low-altitude counterparts, and we speculate that this may enhance their oxygen transport capacity under low-oxygen environments. Thus, TAM-induced RNA diversity may be physiologically significant, providing an alternative strategy in lifestyle evolution.

The Stem Cell Factor Sox2 Is a Positive Timer of Oligodendrocyte Development in the Postnatal Murine Spinal Cord

Myelination in the central nervous system takes place predominantly during the postnatal development of humans and rodents by myelinating oligodendrocytes (OLs), which are differentiated from oligodendrocyte progenitor cells (OPCs). We recently reported that Sox2 is essential for developmental myelination in the murine brain and spinal cord. It is still controversial regarding the role of Sox2 in oligodendroglial lineage progression in the postnatal murine spinal cord. Analyses of a series of cell- and stage-specific Sox2 mutants reveal that Sox2 plays a biphasic role in regulating oligodendroglial lineage progression in the postnatal murine spinal cord. Sox2 controls the number of OPCs for subsequent differentiation through regulating their proliferation. In addition, Sox2 regulates the timing of OL differentiation and modulates the rate of oligodendrogenesis. Our experimental data prove that Sox2 is an intrinsic positive timer of oligodendroglial lineage progression and suggest that interventions affecting oligodendroglial Sox2 expression may be therapeutic for overcoming OPC differentiation arrest in dysmyelinating and demyelinating disorders.

[Analysis of the related factors of attention deficit/hyperactivity disorder and allergic rhinitis in children]

Objective:To investigate the association between symptom of attention deficit/hyperactivity disorder (ADHD) and allergic rhinitis (AR) in children with AR at different sexes and different ages. Method:A total of 439 AR children aged 6 to 12 years were enrolled in this study. Basic information (age, gender, medical history, family history and comorbidities) of children with AR was collected. Results of prick tests on children skin were recorded. (TNSS) and Chinese version of the SNAP-Ⅳ scale, children under the guidance of independent completion of children's quality of life of children with nasal conjunctivitis scale (PRQLQ). According to the results of SNAP-Ⅳ, children were divided into AR with ADHD group ［attention deficit and hyperactivity symptom score (IHS) >1.25］ and AR without ADHD group (IHS≤1.25). The differences between the two groups of children were analyzed using group t-test and χ² test, and the relationship between each parameter and IHS >1.25 was analyzed by binary logistic regression. Result:Using SPSS 22.0 software, among all the included AR children, IHS >1.25 children accounted for 26.4%, IHS >1.25 group AR symptom scores were significantly higher than HIS ≤1.25 groups. Univariate analysis showed that children with age, gender, duration of AR symptoms, skin index and PRQLQ subscales had a correlation with IHS >1.25. After controlling for age and gender, duration of AR symptoms and skin index correlated with IHS >1.25 The estimated OR values are 1.807 (95%CI: 1.350-2.419) and 1.912 (95%CI: 1.320-2.772), respectively. The estimated OR values of PRQLQ subscale and IHS >1.25 were 1.657 (nasal symptom score), 1.324 (eye symptom score), 2.48 (non-eye-nasal symptom score), 1.418 (Behavior problem score) and 2.045 (activity and sleep score). The correlation between IHS>1.25 and the skin index and PRQLQ subscales was mainly found in males with stratification of age and gender, and the association between duration of AR symptoms and HIS >1.25 was statistically significant among all groups reflected. Conclusion:The association between attention deficits and hyperactivity symptoms in AR children was correlated with the severity of AR symptoms, duration, and skin index, and this association was more pronounced in males. In children with AR and ADHD, early management of AR symptoms may improve their ADHD symptoms.

Anaerobic co-digestion of pig manure and food waste; effects on digestate biosafety, dewaterability, and microbial community dynamics

This study assessed the effect of varying pig manure (PM)/food waste (FW) mixing ratio and hydraulic retention time (HRT) on methane yields, digestate dewaterability, enteric indicator bacteria and microbial communities during anaerobic co-digestion. Three 10 L digesters were operated at 39 °C, each with a PM/FW feedstock composition of 85%/15%, 63%/37% and 40%/60% (volatile solids basis). While the PM/FW ratio was different among reactors, the organic loading rate applied was equal, and increased stepwise with reducing HRT. The effects of three different HRTs were studied: 41, 29, and 21 days. Increasing the proportion of FW in the feedstock significantly increased methane yields, but had no significant effect on counts of enteric indicator bacteria in the digestate or specific resistance to filtration, suggesting that varying the PM/FW feedstock composition at the mixing ratios studied should not have major consequences for digestate disposal. Decreasing HRT significantly increased volumetric methane yields, increased digestate volatile solids concentrations and increased the proportion of particles >500 µm in the digestate, indicating that decreasing HRT to 21 days reduced methane conversion efficiency High throughput 16S rRNA sequencing data revealed that microbial communities were just slightly affected by changes in digester operating conditions. These results would provide information useful when optimizing the start-up and operation of biogas plants treating these substrates.

A glimpse of gluons through deeply virtual compton scattering on the proton

The internal structure of nucleons (protons and neutrons) remains one of the greatest outstanding problems in modern nuclear physics. By scattering high-energy electrons off a proton we are able to resolve its fundamental constituents and probe their momenta and positions. Here we investigate the dynamics of quarks and gluons inside nucleons using deeply virtual Compton scattering (DVCS)-a highly virtual photon scatters off the proton, which subsequently radiates a photon. DVCS interferes with the Bethe-Heitler (BH) process, where the photon is emitted by the electron rather than the proton. We report herein the full determination of the BH-DVCS interference by exploiting the distinct energy dependences of the DVCS and BH amplitudes. In the regime where the scattering is expected to occur off a single quark, measurements show an intriguing sensitivity to gluons, the carriers of the strong interaction.

Large-scale study of clinical and biochemical characteristics of Chinese patients diagnosed with Krabbe disease

Krabbe disease (KD) is a rare disease caused by the deficiency of β-galactocerebrosidase. This study investigated 22 unrelated Chinese patients, including their clinical presentations, plasma psychosine levels and β-galactocerebrosidase gene mutations. We found the late-onset form of KD present in 82% of the patients in our study, which was more prevalent than in patients from other populations. Plasma psychosine levels were elevated in KD, which were correlated with the severity of clinical presentations. Sanger sequencing identified 8 novel mutations, including 7 missense mutations, p.H253Y, p.S259L, p.P318L, p.F350V, p.T428A, p.L530P, p.G586D, and 1 splicing mutation, c.1251+1G>A. Quantitative real-time polymerase chain reaction (PCR) and multiplex ligation-dependent probe amplification identified a novel exon 12 and 14 deletion, separately. Next generation sequencing, applied at the final step, revealed 2 missense mutant alleles missed using Sanger sequencing. The most common mutation in Chinese population is p.P154H, which accounts for 20.5% of alleles. Consistent with the higher prevalence of the late-onset form of KD, missense mutations predominated in our study, different with the common mutation types in Europe and Japan. This work was the first large-scale study of Chinese KD patients describing their clinical, biochemical and genetic characteristics, which furthered our understanding of this classical neurological lysosomal storage disease.

Differential expression of miR16 in glioblastoma and glioblastoma stem cells: their correlation with proliferation, differentiation, metastasis and prognosis

The function of miR16 in multiforme glioblastoma multiforme (GBM) and its stem cells (GSCs) remains elusive. To this end, we investigated the patterns of miR16 expression in these cells and their correlation with malignant behaviors and clinical outcomes. The levels of miR16 and its targeted genes in tumor tissue of GBM and GBM SGH44, U87, U251 cells as well as their stem cell counterparts were measured by qRT–PCR or western blot or immunohistochemistry. Luciferase reporter assay was used to confirm the binding of miR16 to 3′-UTR of its target genes. The effects of miR16 on malignant behaviors were investigated, including tumor cell viability, soft-agar colony formation, GSCs Matrigel colony forming and migration and invasion as well as nude mice xenograft model. Differentially expression patterns of miR16 in glioblastoma cells and GSCs cells were found in this study. Changes of miR16 targeted genes, Bcl2 (B cell lymphoma 2), CDK6 (Cyclin-dependent kinase 6), CCND1 (cyclin D1), CCNE1 (cyclin E1) and SOX5 were confirmed in glioblastoma cell lines and tissue specimens. In vitro and in vivo studies showed that tumor cell proliferation was inhibited by miR16 mimic, but enhanced by miR16 inhibitor. The expression level of miR16 positively correlates with GSCs differentiation, but negatively with the abilities of migration, motility, invasion and colony formation in glioblastoma cells. The inhibitory effects of miR16 on its target genes were also found in nude mice xenograft model. Our findings revealed that the miR16 functions as a tumor suppressor in GSCs and its association with prognosis in GBM.

Mitochondrial complex I bridges a connection between regulation of carbon flexibility and gastrointestinal commensalism in the human fungal pathogen Candida albicans

Efficient assimilation of alternative carbon sources in glucose-limited host niches is critical for colonization of Candida albicans, a commensal yeast that frequently causes opportunistic infection in human. C. albicans evolved mechanistically to regulate alternative carbon assimilation for the promotion of fungal growth and commensalism in mammalian hosts. However, this highly adaptive mechanism that C. albicans employs to cope with alternative carbon assimilation has yet to be clearly understood. Here we identified a novel role of C. albicans mitochondrial complex I (CI) in regulating assimilation of alternative carbon sources such as mannitol. Our data demonstrate that CI dysfunction by deleting the subunit Nuo2 decreases the level of NAD⁺, downregulates the NAD⁺-dependent mannitol dehydrogenase activity, and consequently inhibits hyphal growth and biofilm formation in conditions when the carbon source is mannitol, but not fermentative sugars like glucose. Mannitol-dependent morphogenesis is controlled by a ROS-induced signaling pathway involving Hog1 activation and Brg1 repression. In vivo studies show that nuo2Δ/Δ mutant cells are severely compromised in gastrointestinal colonization and the defect can be rescued by a glucose-rich diet. Thus, our findings unravel a mechanism by which C. albicans regulates carbon flexibility and commensalism. Alternative carbon assimilation might represent a fitness advantage for commensal fungi in successful colonization of host niches.

Most fermentative sugars like glucose, although routinely used in laboratory cell culture medium, are in fact only present at very low levels and even absent in many host niches. Therefore, assimilation of alternative nutrients is essential for the survival, proliferation and infection of most clinically important microbial pathogens like C. albicans in their hosts. In this study, we show that mitochondrial complex I (CI) is indispensable for proper hyphal growth and biofilm formation of C. albicans cells when mannitol, but not fermentative sugars like glucose or mannose, is used as the sole carbon source. We also find that a specific signaling pathway that senses and responds to the alternative carbon source incorporates input from mitochondrially-derived molecules like reactive oxygen species (ROS) to influence activation of the Hog1 MAPK and expression of the biofilm-regulator Brg1. Our findings further demonstrate that CI dysfunction confers a severe defect of C. albicans in gastrointestinal colonization and changing the diet with glucose is able to significantly rescue the commensal defect. Our study suggests that C. albicans has a unique regulatory system to sense and utilize the alternative carbon sources abundant in the GI tract and to promote commensalism. Significantly, CI activity appears to play a vital role in this highly adaptive system to regulate commensalism, in addition to its well-characterized role in virulence.

Population transcriptomes reveal synergistic responses of DNA polymorphism and RNA expression to extreme environments on the Qinghai-Tibetan Plateau in a predatory bird

Low oxygen and temperature pose key physiological challenges for endotherms living on the Qinghai-Tibetan Plateau (QTP). Molecular adaptations to high-altitude living have been detected in the genomes of Tibetans, their domesticated animals and a few wild species, but the contribution of transcriptional variation to altitudinal adaptation remains to be determined. Here we studied a top QTP predator, the saker falcon, and analysed how the transcriptome has become modified to cope with the stresses of hypoxia and hypothermia. Using a hierarchical design to study saker populations inhabiting grassland, steppe/desert and highland across Eurasia, we found that the QTP population is already distinct despite having colonized the Plateau <2000 years ago. Selection signals are limited at the cDNA level, but of only seventeen genes identified, three function in hypoxia and four in immune response. Our results show a significant role for RNA transcription: 50% of upregulated transcription factors were related to hypoxia responses, differentiated modules were significantly enriched for oxygen transport, and importantly, divergent EPAS1 functional variants with a refined co-expression network were identified. Conservative gene expression and relaxed immune gene variation may further reflect adaptation to hypothermia. Our results exemplify synergistic responses between DNA polymorphism and RNA expression diversity in coping with common stresses, underpinning the successful rapid colonization of a top predator onto the QTP. Importantly, molecular mechanisms underpinning highland adaptation involve relatively few genes, but are nonetheless more complex than previously thought and involve fine-tuned transcriptional responses and genomic adaptation.