Ion Competition in Condensed DNA Arrays in the Attractive Regime

Physical origin of DNA condensation by multivalent cations remains unsettled. Here, we report quantitative studies of how one DNA-condensing ion (Cobalt³⁺ Hexammine, or Co³⁺Hex) and one nonDNA-condensing ion (Mg²⁺) compete within the interstitial space in spontaneously condensed DNA arrays. As the ion concentrations in the bath solution are systematically varied, the ion contents and DNA-DNA spacings of the DNA arrays are determined by atomic emission spectroscopy and x-ray diffraction, respectively. To gain quantitative insights, we first compare the experimentally determined ion contents with predictions from exact numerical calculations based on nonlinear Poisson-Boltzmann equations. Such calculations are shown to significantly underestimate the number of Co³⁺Hex ions, consistent with the deficiencies of nonlinear Poisson-Boltzmann approaches in describing multivalent cations. Upon increasing the concentration of Mg²⁺, the Co³⁺Hex-condensed DNA array expands and eventually redissolves as a result of ion competition weakening DNA-DNA attraction. Although the DNA-DNA spacing depends on both Mg²⁺ and Co³⁺Hex concentrations in the bath solution, it is observed that the spacing is largely determined by a single parameter of the DNA array, the fraction of DNA charges neutralized by Co³⁺Hex. It is also observed that only ∼20% DNA charge neutralization by Co³⁺Hex is necessary for spontaneous DNA condensation. We then show that the bath ion conditions can be reduced to one variable with a simplistic ion binding model, which is able to describe the variations of both ion contents and DNA-DNA spacings reasonably well. Finally, we discuss the implications on the nature of interstitial ions and cation-mediated DNA-DNA interactions.     

Long non‐coding PANDAR as a novel biomarker in human cancer: A systematic review

Objectives

Long non‐coding RNAs (lncRNAs) are characterized as a group of RNAs that more than 200 nucleotides in length and have no protein‐coding function. More and more evidences provided that lncRNAs serve as key molecules in the development of cancer. Deregulation of lncRNAs functions as either oncogenes or tumour suppressor genes in various diseases. Recently, increasing studies about PANDAR in cancer progression were reported. In our review, we will focus on the current research on the character of PANDAR include the clinical management, tumour progression and molecular mechanisms in human cancers.

Materials and methods

We summarize and analyze current studies concerning the biological functions and mechanisms of lncRNA PANDA in tumour development. The related studies were obtained through a systematic search of Pubmed.

Results

PANDAR was a well‐characterized oncogenic lncRNA and widely overexpressed in many tumours. PANDAR is upregulated in many types of cancer, including colorectal cancer, lung cancer, renal cell carcinoma, cholangiocarcinoma, osteosarcoma, thyroid cancer and other cancers. Upregulation of PANDAR was significantly associated with advanced tumour weights, TNM stage and overall survival. Furthermore, repressed of PANDAR would restrain proliferation, migration and invasion.

Conclusion

PANDAR may act as a powerful tumour biomarker for cancer diagnosis and treatment.     

AFAP1‐AS1: A novel oncogenic long non‐coding RNA in human cancers

Long non‐coding RNAs (lncRNAs), a group of non‐protein‐coding RNAs with more than 200 nucleotides in length, are involved in multiple biological processes, such as the proliferation, apoptosis, migration and invasion. Moreover, numerous studies have shown that lncRNAs play important roles as oncogenes or tumour suppressor genes in human cancers. In this paper, we concentrate on actin filament‐associated protein 1‐antisense RNA 1 (AFAP1‐AS1), a well‐known long non‐coding RNA that is overexpressed in various tumour tissues and cell lines, including oesophageal cancer, pancreatic ductal adenocarcinoma, nasopharyngeal carcinoma, lung cancer, hepatocellular carcinoma, ovarian cancer, colorectal cancer, biliary tract cancer and gastric cancer. Moreover, high expression of AFAP1‐AS1 was associated with the clinicopathological features and cancer progression. In this review, we sum up the current studies on the characteristics of AFAP1‐AS1 in the biological function and mechanism of human cancers.     

2004年新疆旧石器考古调查简报

2004年5-6月,中国科学院古脊椎动物与古人类研究所和新疆文物考古研究所联合组队,在新疆北部和中部进行了旧石器时代考古调查。发现24个石器地点和数千件石制品,采集和试掘出500余件石制品;绝大多数石制品来自于地表,少数出自原生地层。石制品类型多样,包括普通石核与石片、棱柱状石核、石叶、两面器、细石叶石核、细石叶、勒瓦娄哇石核与石片等;原料种类多样,尺寸、形态、技术变异大。从技术与类型判断,这些不同地点的文化材料时代跨度较大,较早的可能属旧石器时代晚期之初,甚至旧石器时代中期,较晚的则可能属于新石器时代早中期。较早阶段的石制品组合与中亚、西伯利亚阿尔泰地区同期遗址的文化面貌有相似之处,也与我国水洞沟遗址的石叶遗存有一定联系。骆驼石遗址及其丰富的勒瓦娄哇制品及大型石叶制品是本次调查的最大收获。本次调查的成果表明,新疆地区在旧石器时代晚期是人类迁徙和生存演化的活跃地带,留下丰富的文化遗存,对研究当时人类技术、文化特点和适应生存能力提供了重要材料与信息;很多地点具有与欧洲、俄罗斯阿尔泰地区旧石器时代中、晚期相似的文化遗存,对研究当时欧亚大陆古人群的迁徙、融合和文化交流具有重要价值;该地区具有发现更多、更重要的旧石器时代遗址并开展深入的考古发掘与研究的巨大潜力。     

山东日照黄泥梁旧石器时代遗址发掘简报

黄泥梁旧石器时代遗址埋藏于山东省日照市丝山东麓的黄土台地中,2006年发现,2011、2012年进行复查和试掘,2013年正式发掘,发掘面积约50 m2。遗址文化层厚约1.2m,位于地表下3-4m处,经光释光测定,文化层的年代为54-59 kaBP。本次发掘出土有编号的石制品1876件,包括石核、石片、石锤、工具、断块等,此外还有大量的碎屑类石制品。石料主要为脉石英和安山岩两种,大多就地取材。石制品类型以石片、断块为主,石核有一定比例,石锤上的打击痕迹明显,工具数量较少,以简单加工的刮削器为主。石制品的剥片、加工技术均为硬锤直接打击法。初步分析表明黄泥梁遗址为一处原地埋藏的石器制作场所。     

Development of continuous microwave-assisted protein digestion with immobilized enzyme

In this study, an easy and efficiency protein digestion method called continuous microwave-assisted protein digestion (cMAED) with immobilized enzyme was developed and applied for proteome analysis by LC–MSⁿ. Continuous microwave power outputting was specially designed and applied. Trypsin and bromelain were immobilized onto magnetic micropheres. To evaluate the method of cMAED, bovine serum albumin (BSA) and protein extracted from ginkgo nuts were used as model and real protein sample to verify the digestion efficiency of cMAED. Several conditions including continuous microwave power, the ratio of immobilized trypsin/BSA were optimized according to the analysis of peptide fragments by Tricine SDS–PAGE and LC–MSⁿ. Subsequently, the ginkgo protein was digested with the protocols of cMAED, MAED and conventional heating enzymatic digestion (HED) respectively and the LC–MSⁿ profiles of the hydrolysate was compared. Results showed that cMAED combined with immobilized enzyme was a fast and efficient digestion method for protein digestion and microwave power tentatively affected the peptide producing. The cMAED method will be expanded for large-scale preparation of bioactive peptides and peptide analysis in biological and clinical research.     

Histomorphometric analysis of adult articular calcified cartilage zone

The aim of this study was to carry out a histomorphometric analysis of calcified cartilage zone (CCZ) and its interfaces between hyaline cartilage and subchondral bone. The study used 40 donated normal human femoral condyles, from which paraffin-embedded sections were prepared after fixation and decalcification. The histomorphology of the CCZ were qualitatively and quantitatively observed by staining, scanning electron microscopy (SEM) and three-dimensional (3D) reconstruction. The hyaline cartilage and CCZ were stained red with Safranin-O, and the subchondral bone was stained blue with Fast green. CCZ was stained black after von Kossa staining. The hyaline cartilage was interlocked tightly in the manner of “ravine-engomphosis” by the CCZ. The surface roughnesses of tidemark and cement line were 1.14 ± 0.04 and 1.99 ± 0.38. The maximum, minimum and mean thicknesses of CCZ were 277.12 ± 8.6, 9.83 ± 6.72 and 104.162 ± 0.87 μm, respectively. The cell density of CCZ (51.25 ± 21.26 cells/mm²) was significantly lower than that of the hyaline cartilage (152.54 ± 35.77 cells/mm²) (P < 0.05). The subchondral bone was anchored tightly in the manner of a “comb-anchor” by the CCZ in our 3D reconstruction model. Thus, we discovered two junctional interfaces of CCZ using different histomorphometric methods. The upper interface of CCZ is a “ravine-engomphosis” shape, while its lower interface is a “comb-anchor” shape.     

Characterizing DNA condensation and conformational changes in organic solvents

Organic solvents offer a new approach to formulate DNA into novel structures suitable for gene delivery. In this study, we examined the in situ behavior of DNA in N, N-dimethylformamide (DMF) at low concentration via laser light scattering (LLS), TEM, UV absorbance and Zeta potential analysis. Results revealed that, in DMF, a 21bp oligonucleotide remained intact, while calf thymus DNA and supercoiled plasmid DNA were condensed and denatured. During condensation and denaturation, the size was decreased by a factor of 8-10, with calf thymus DNA forming spherical globules while plasmid DNA exhibited a toroid-like conformation. In the condensed state, DNA molecules were still able to release the counterions to be negatively charged, indicating that the condensation was mainly driven by the excluded volume interactions. The condensation induced by DMF was reversible for plasmid DNA but not for calf thymus DNA. When plasmid DNA was removed from DMF and resuspended in an aqueous solution, the DNA was quickly regained a double stranded configuration. These findings provide further insight into the behavior and condensation mechanism of DNA in an organic solvent and may aid in developing more efficient non-viral gene delivery systems.     

内蒙古扎赉诺尔蘑菇山北遗址2019年调查报告

蘑菇山北遗址位于内蒙古自治区呼伦贝尔市扎赉诺尔区蘑菇山一带,发现于1980年,同年和1990年两次采集和试掘,获得了比较丰富的石制品,是中国东北地区一处重要的旧石器时代晚期遗址。2019年8月进行了新的调查和试掘,获得石制品近400件,主要分布于地表和地层表土的角砾堆积中,全部为打制产品,原料为就地取材的安山岩,类型包括石核、石片、断块和石器等;石器器型较大,技术成熟,主要属于石片石器工业。试掘的T3探方出土了丰富的打制石制品,以小型石片为主,是该遗址的新收获。根据石制品的技术特点和类型组合分析,该遗址的年代应为旧石器时代晚期。