Giant panda BAC library construction and assembly of a 650-kb contig spanning major histocompatibility complex class II region

<p>Abstract</p> <p>Background</p> <p>Giant panda is rare and endangered species endemic to China. The low rates of reproductive success and infectious disease resistance have severely hampered the development of captive and wild populations of the giant panda. The major histocompatibility complex (MHC) plays important roles in immune response and reproductive system such as mate choice and mother-fetus bio-compatibility. It is thus essential to understand genetic details of the giant panda MHC. Construction of a bacterial artificial chromosome (BAC) library will provide a new tool for panda genome physical mapping and thus facilitate understanding of panda MHC genes.</p> <p>Results</p> <p>A giant panda BAC library consisting of 205,800 clones has been constructed. The average insert size was calculated to be 97 kb based on the examination of 174 randomly selected clones, indicating that the giant panda library contained 6.8-fold genome equivalents. Screening of the library with 16 giant panda PCR primer pairs revealed 6.4 positive clones per locus, in good agreement with an expected 6.8-fold genomic coverage of the library. Based on this BAC library, we constructed a contig map of the giant panda MHC class II region from <it>BTNL2 </it>to <it>DAXX </it>spanning about 650 kb by a three-step method: (1) PCR-based screening of the BAC library with primers from homologous MHC class II gene loci, end sequences and BAC clone shotgun sequences, (2) DNA sequencing validation of positive clones, and (3) restriction digest fingerprinting verification of inter-clone overlapping.</p> <p>Conclusion</p> <p>The identifications of genes and genomic regions of interest are greatly favored by the availability of this giant panda BAC library. The giant panda BAC library thus provides a useful platform for physical mapping, genome sequencing or complex analysis of targeted genomic regions. The 650 kb sequence-ready BAC contig map of the giant panda MHC class II region from <it>BTNL2 </it>to <it>DAXX</it>, verified by the three-step method, offers a powerful tool for further studies on the giant panda MHC class II genes.</p

Single-nucleotide polymorphism-gene intermixed networking reveals co-linkers connected to multiple gene expression phenotypes

Gene expression profiles and single-nucleotide polymorphism (SNP) profiles are modern data for genetic analysis. It is possible to use the two types of information to analyze the relationships among genes by some genetical genomics approaches. In this study, gene expression profiles were used as expression traits. And relationships among the genes, which were co-linked to a common SNP(s), were identified by integrating the two types of information. Further research on the co-expressions among the co-linked genes was carried out after the gene-SNP relationships were established using the Haseman-Elston sib-pair regression. The results showed that the co-expressions among the co-linked genes were significantly higher if the number of connections between the genes and a SNP(s) was more than six. Then, the genes were interconnected via one or more SNP co-linkers to construct a gene-SNP intermixed network. The genes sharing more SNPs tended to have a stronger correlation. Finally, a gene-gene network was constructed with their intensities of relationships (the number of SNP co-linkers shared) as the weights for the edges

Dynamic cerebral blood flow assessment based on electromagnetic coupling sensing and image feature analysis

Dynamic assessment of cerebral blood flow (CBF) is crucial for guiding personalized management and treatment strategies, and improving the prognosis of stroke. However, a safe, reliable, and effective method for dynamic CBF evaluation is currently lacking in clinical practice. In this study, we developed a CBF monitoring system utilizing electromagnetic coupling sensing (ECS). This system detects variations in brain conductivity and dielectric constant by identifying the resonant frequency (RF) in an equivalent circuit containing both magnetic induction and electrical coupling. We evaluated the performance of the system using a self-made physical model of blood vessel pulsation to test pulsatile CBF. Additionally, we recruited 29 healthy volunteers to monitor cerebral oxygen (CO), cerebral blood flow velocity (CBFV) data and RF data before and after caffeine consumption. We analyzed RF and CBFV trends during immediate responses to abnormal intracranial blood supply, induced by changes in vascular stiffness, and compared them with CO data. Furthermore, we explored a method of dynamically assessing the overall level of CBF by leveraging image feature analysis. Experimental testing substantiates that this system provides a detection range and depth enhanced by three to four times compared to conventional electromagnetic detection techniques, thereby comprehensively covering the principal intracranial blood supply areas. And the system effectively captures CBF responses under different intravascular pressure stimulations. In healthy volunteers, as cerebral vascular stiffness increases and CO decreases due to caffeine intake, the RF pulsation amplitude diminishes progressively. Upon extraction and selection of image features, widely used machine learning algorithms exhibit commendable performance in classifying overall CBF levels. These results highlight that our proposed methodology, predicated on ECS and image feature analysis, enables the capture of immediate responses of abnormal intracranial blood supply triggered by alterations in vascular stiffness. Moreover, it provides an accurate diagnosis of the overall CBF level under varying physiological conditions

Super-acceleration on the Brane by Energy Flow from the Bulk

We consider a brane cosmological model with energy exchange between brane and bulk. Parameterizing the energy exchange term by the scale factor and Hubble parameter, we are able to exactly solve the modified Friedmann equation on the brane. In this model, the equation of state for the effective dark energy has a transition behavior changing from $w_{de}^{eff}>-1$ to $w_{de}^{eff}<-1$, while the equation of state for the dark energy on the brane has $w>-1$. Fitting data from type Ia supernova, Sloan Digital Sky Survey and Wilkinson Microwave Anisotropy Probe, our universe is predicted now in the state of super-acceleration with $w_{de0}^{eff}=-1.21$.Comment: Revtex, 11 pages including 2 figures,v2: tpos fixed, references added, to appear in JCA

The CDEX-1 1 kg Point-Contact Germanium Detector for Low Mass Dark Matter Searches

The CDEX Collaboration has been established for direct detection of light dark matter particles, using ultra-low energy threshold p-type point-contact germanium detectors, in China JinPing underground Laboratory (CJPL). The first 1 kg point-contact germanium detector with a sub-keV energy threshold has been tested in a passive shielding system located in CJPL. The outputs from both the point-contact p+ electrode and the outside n+ electrode make it possible to scan the lower energy range of less than 1 keV and at the same time to detect the higher energy range up to 3 MeV. The outputs from both p+ and n+ electrode may also provide a more powerful method for signal discrimination for dark matter experiment. Some key parameters, including energy resolution, dead time, decay times of internal X-rays, and system stability, have been tested and measured. The results show that the 1 kg point-contact germanium detector, together with its shielding system and electronics, can run smoothly with good performances. This detector system will be deployed for dark matter search experiments.Comment: 6 pages, 8 figure

Quasinormal modes of black holes absorbing dark energy

We study perturbations of black holes absorbing dark energy. Due to the accretion of dark energy, the black hole mass changes. We observe distinct perturbation behaviors for absorption of different forms of dark energy into the black holes. This provides the possibility of extracting information whether dark energy lies above or below the cosmological constant boundary $w=-1$. In particular, we find in the late time tail analysis that, differently from the other dark energy models, the accretion of phantom energy exhibits a growing mode in the perturbation tail. The instability behavior found in this work is consistent with the Big Rip scenario, in which all of the bound objects are torn apart with the presence of the phantom dark energy.Comment: 11 pages, 5 figures, revised version, accepted for publication in Phys.Lett.

Calibration of the Timing Performance of GECAM-C

As a new member of the Gravitational wave high-energy Electromagnetic Counterpart All-sky Monitor (GECAM) after GECAM-A and GECAM-B, GECAM-C (originally called HEBS), which was launched on board the SATech-01 satellite on July 27, 2022, aims to monitor and localize X-ray and gamma-ray transients from $\sim$ 6 keV to 6 MeV. GECAM-C utilizes a similar design to GECAM but operates in a more complex orbital environment. In this work, we utilize the secondary particles simultaneously produced by the cosmic-ray events on orbit and recorded by multiple detectors, to calibrate the relative timing accuracy between all detectors of GECAM-C. We find the result is 0.1 $\mu \rm s$, which is the highest time resolution among all GRB detectors ever flown and very helpful in timing analyses such as minimum variable timescale and spectral lags, as well as in time delay localization. Besides, we calibrate the absolute time accuracy using the one-year Crab pulsar data observed by GECAM-C and Fermi/GBM, as well as GECAM-C and GECAM-B. The results are $2.02\pm 2.26\ \mu \rm s$ and $5.82\pm 3.59\ \mu \rm s$, respectively. Finally, we investigate the spectral lag between the different energy bands of Crab pulsar observed by GECAM and GBM, which is $\sim -0.2\ {\rm \mu s\ keV^{-1}}$.Comment: submitte

The Childhood Acute Illness and Nutrition (CHAIN) network nested case-cohort study protocol: a multi-omics approach to understanding mortality among children in sub-Saharan Africa and South Asia

Introduction: Many acutely ill children in low- and middle-income settings have a high risk of mortality both during and after hospitalisation despite guideline-based care. Understanding the biological mechanisms underpinning mortality may suggest optimal pathways to target for interventions to further reduce mortality. The Childhood Acute Illness and Nutrition (CHAIN) Network ( www.chainnnetwork.org) Nested Case-Cohort Study (CNCC) aims to investigate biological mechanisms leading to inpatient and post-discharge mortality through an integrated multi-omic approach. Methods and analysis; The CNCC comprises a subset of participants from the CHAIN cohort (1278/3101 hospitalised participants, including 350 children who died and 658 survivors, and 270/1140 well community children of similar age and household location) from nine sites in six countries across sub-Saharan Africa and South Asia. Systemic proteome, metabolome, lipidome, lipopolysaccharides, haemoglobin variants, toxins, pathogens, intestinal microbiome and biomarkers of enteropathy will be determined. Computational systems biology analysis will include machine learning and multivariate predictive modelling with stacked generalization approaches accounting for the different characteristics of each biological modality. This systems approach is anticipated to yield mechanistic insights, show interactions and behaviours of the components of biological entities, and help develop interventions to reduce mortality among acutely ill children. Ethics and dissemination. The CHAIN Network cohort and CNCC was approved by institutional review boards of all partner sites. Results will be published in open access, peer reviewed scientific journals and presented to academic and policy stakeholders. Data will be made publicly available, including uploading to recognised omics databases. Trial registration NCT03208725