Force spectroscopy and fluorescence microscopy of dsDNA–YOYO-1 complexes: implications for the structure of dsDNA in the overstretching region

When individual dsDNA molecules are stretched beyond their B-form contour length, they reveal a structural transition in which the molecule extends 1.7 times its contour length. The nature of this transition is still a subject of debate. In the first model, the DNA helix unwinds and combined with the tilting of the base pairs (which remain intact), results in a stretched form of DNA (also known as S-DNA). In the second model the base pairs break resulting effectively in two single-strands, which is referred to as force-induced melting. Here a combination of optical tweezers force spectroscopy with fluorescence microscopy was used to study the structure of dsDNA in the overstretching regime. When dsDNA was stretched in the presence of 10 nM YOYO-1 an initial increase in total fluorescence intensity of the dye–DNA complex was observed and at an extension where the dsDNA started to overstretch the fluorescence intensity leveled off and ultimately decreased when stretched further into the overstretching region. Simultaneous force spectroscopy and fluorescence polarization microscopy revealed that the orientation of dye molecules did not change significantly in the overstretching region (78.0°± 3.2°). These results presented here clearly suggest that, the structure of overstretched dsDNA can be explained accurately by force induced melting.     

Biological and biochemical properties of the small viral RNA(pRNA) essential for the packaging of the dsDNA of phage ø29

The genome of the lineal double-stranded DNA viruses of both prokaryotes and eukaryotes is packaged into a preformed procapsid during maturation. Common features exist in this step of the viral life cycle. Bacteriophage ø29 is an ideal model in this study because its DNA can be efficiently packaged in vitro with all components overproduced and purified. An exciting aspect is the discovery that a small viral RNA (pRNA) encoded by ø29 has a novel and essential role in viral DNA packaging. This pRNA is not a structural component of the mature virion, nor is it required for the assembly of the procapsid. The discovery of pRNA as a non-protein participant in viral DNA packaging extends previously demonstrated RNA functions.     

DRE顺式作用元件dsDNA芯片制备

DRE顺式作用元件能与DREB转录因子特异结合,在诱导逆境（干旱、高盐、低温）基因表达过程中起重要作用。dsDNA（double strand DNA）微阵列芯片技术能够有效地检测序列特异性DNA结合蛋白质（转录因子）与大量DNA靶点（顺式作用元件）的特异性结合,可有效分析生物分子结合作用。根据DRE顺式作用元件核心序列设计并化学合成含发夹结构的单链DNA探针,采用Taq DNA聚合酶在片延伸,并对其在片延伸体系的反应温度、Mg^2＋浓度以及单链探针是否变性等条件进行了优化。结果表明,50％的反应温度,2．5mmol／L的Mg^2＋浓度和单链不变性是TaqDNA聚合酶在片延伸的最佳条件。优化方法制备的dsDNA芯片将更有利于DRE顺式作用元件与DREB抗逆转录因子相互作用的研究。     

PhageGT：dsDNA噬菌体基因组末端分析软件

【背景】随着测序费用的降低,越来越多的科学家选择利用高通量测序技术研究噬菌体的基因组序列。通过对这些基因组数据的分析和研究,一些科学家也开发出了判断dsDNA噬菌体末端序列的方法,但这些方法是基于Linux系统下的命令,并没有在Windows操作系统下的软件。【目的】在Windows平台下开发一款免费的、可以在高通量测序获得的庞大序列文件中找到dsDNA噬菌体基因组末端序列的软件PhageGT。【方法】使用Visual Studio 2019开发一个基于对话框的微软基础类库(Microsoft Foundation Classes,MFC)应用程序。软件使用C++语言开发,逐行读取序列文件中的每条Reads,并设计相应的算法进行统计、计算。【结果】软件PhageGT可在高通量测序文件中提取出不同序列出现的频率、排序,并利用提取序列的最高频率和序列平均频率的比值(R值)判断噬菌体基因组是否存在末端序列。【结论】软件PhageGT的使用比较方便、简单。软件PhageGT和本文所利用的所有测试数据均可从https://zenodo.org/record/4674231#.YHADb-gzZxc免费获得。     

Age-related Changes in the Insulin Receptor β in the Gerbil Hippocampus

The insulin receptor has been reported to be associated with memory formation via the hippocampus. In this study, we observed age-related changes in the insulin receptor β immunoreactivity and its protein levels in the hippocampus of gerbils of various ages in order to identify the correlation between the insulin receptor β and aging processes in the hippocampus. Insulin receptor β immunoreactivity was mainly detected in the molecular and polymorphic layers of the dentate gyrus, and in mossy fibers, Schaffer collaterals, alveus and stratum lacunosum-moleculare of the hippocampus proper (CA1-3) of gerbils at postnatal month 1 (PM 1). Insulin receptor β immunoreactivity decreased with age in all of these structures, except for the alveus. Reduction of the insulin receptor β immunoreactivity was prominent in the molecular layer of the dentate gyrus at PM 6 and in the stratum lacunosum-moleculare of the CA1 region at PM 12, while insulin receptor β immunoreactivity was decreased in other regions in the PM 18 groups. In addition, insulin receptor β protein level in the whole hippocampus was slightly increased at PM 3, and it decreased in an age-dependent manner from PM 6 to PM 24. These reductions of the insulin receptor β in the hippocampus may be associated with age-related memory deficits in gerbils.     

SH groups in the α-naphthyl acetate esterase in the thyroid of the guinea-pig

Summary The -naphthyl acetate esterase in both group I and group II thyroid cells is shown to contain SH groups since there is a decline in activity in both cell groups when certain sulfhydryl reagents [DTNB; 5,5-Dithiobis-(2-nitrobenzoic acid)-AgNO₃-Mersalyl-PCMB (parachloro mercuribenzoate)+urea] are added to the incubation media. Thus the inhibition is by far the greatest in group I cells, which also show the greatest activity after incubation in conventional media, when long fixation and storage times are used. In all cases the inhibiting effect was complete or almost completely reversed if cysteine was added to the incubation media in equivalent concentrations to the SH blocker. There were great differences among the sulfhydryl reagents used in their ability to bring about enzyme inhibition. The alkylating agents NEM (N-ethylmaleimide) and iodoacetamide had no or little effect while PCMB could only inhibit the activity of the -naphthylacetate esterase if the enzyme was denaturated with 5 m urea. The maximal inhibitory effect of PCMB was only obtained when NaCl was added to the incubation media. The most effective inhibitor was AgNO₃.     

dsDNA—蛋白质相互识别的结构模型

核酸同蛋白质之间的相互识别是生命的核心过程之一。核酸同蛋白质相互识别取决于核酸的状态。本文在不考虑核酸构象变化的情况下,讨论了dsDNA-蛋白质相互识别。根据dsDNA-蛋白质相互识别的基本结构部件,基本因素,识别信号,探讨了“一般识别”和“特殊识别”的结构模型和“识别词典”问题。     

dsDNA芯片的DNA结合蛋白质计算机模拟系统

dsDNA芯片(double-stranded DNA microarray)是用于DNA结合蛋白质表达研究的新技术,应用一种新的dsDNA芯片制作方法,研究了dsDNA探针设计,开发了相应的计算机模拟系统—DBP软件。可实现芯片上dsDNA探针的选取以及DNA结合蛋白质检测的实验过程模拟,功能包括模拟酶切、模拟电泳、模拟杂交等实验环节。DBP系统包括了可以不断完善的DNA结合蛋白质数据库。对研究dsDNA芯片,检测和分析在生物 体中DNA结合蛋白质的表达谱,揭示细胞的分化和凋亡、信号转导、DNA转录调控的分子机制有重要意义。     

Zooplankton in the ponds with tropical plants in the greenhouses of the Botanical Garden of the Jagiellonian University in Kraków

The presence of P. tetraurelia was found in the pond in "The Palm-House" greenhouse.     

Is neurotensin in the brain involved in thermoregulation of the monkey?

Cannulae for intracerebroventricular (ICV) infusion were implanted stereotaxically in monkeys (Macaca fasicularis) maintained post-operatively in a primate restraint chair. During each experiment, a series of physiological measures was recorded simultaneously on a polygraph which included colonic temperature, vasomotor tone, heart rate, respiratory rate, and basal metabolism as reflected by O₂ uptake. The ICV infusion in a volume of 0.5 ml of neurotensin (NT) in doses ranging from 3–150 μg produced neither a statistically significant nor consistent change in body temperature or vasomotor response. Although the highest dose of 450 μg NT infused ICV caused an immediate bradycardia and a concomitant decline in metabolic and respiratory rates, an average decline in core temperature of 0.6°C and the accompanying cutaneous vasodilation often had a latency as long as 1.0 hr. In contrast to the typical hypothermia in this species following an ICV infusion of catecholamines, implicated in the central pathways underlying thermoregulation, NT failed to elicit a coordinated set of physiological responses for heat dissipation in the monkey. Therefore, it is unlikely that this tridecapeptide plays a role in the central mechanisms mediating the control of body temperature of this primate species.     

Changes in the rate of photosynthesis accompanying the yield increase in wheat cultivars released in the past 50 years

Photosynthetic rates in different development stages were carefully investigated in 18 cultivars of winter wheat released in the period between 1945 and 1995 in the area of Beijing, China. During this period, the recorded grain yield has increased eightfold. However, when those cultivars were planted and managed in the same environment, the difference was reduced to only 36%, indicating that agronomic practices are the most important factors for grain yield. Agronomic features have changed greatly in the past 50 years, through increasing the harvest index (R²=0.89, P<0.05), shortening plant height (R²=0.77, P<0.05) and slightly increasing flag leaf areas (R²=0.45, P<0.05), which is mostly in agreement with many other researchers. In contrast to many reports, however, this study found a genetic increase in the rate of photosynthesis per unit leaf area. From the mid-stem elongation to soft dough stages, the average photosynthetic rates at saturated photosynthetic photon flux density (P_sat) increased by 44%. In the process, the stomatal conductance (g_s) also increased by 122%. Grain yield was positively related to the mean values of P_sat (R²=0.61, P<0.01) and g_s (R²=0.67, P<0.01) in the six development stages. Our experiment may suggest that increase in grain yield was associated with the elevation of leaf photosynthetic rate and stomatal conductance over the past 50 years.     

Variation in the cell cycle time in the crypts of lieberkühn of the mouse

The durations of the phases of the cell cycle were measured at different levels in the jejunal crypts of male Balb/c mice. A mean cell cycle time of 12.3 h was found for the whole crypt. In cell positions 1 and 2, the cell cycle time was 16.7 h, and this time steadily decreased to a value of between 10 and 11 h for cell positions above 11. It is concluded that basally situated crypt cells in the mouse are cycling relatively slowly, and that they form the functional stem cell pool for the crypt. These cells may also compose the potential stem cell pool which repopulates the crypt after death of proliferative cells.     

Every species is good in its season: Do the shifts in the annual temperature dynamics affect the phenology of the zooplankton species in the White Sea?

We hypothesize that shifts in the annual pattern of the environmental parameters may affect the phenology of the zooplankton especially in temperate and polar areas. Five species (cold-water: Calanus glacialis, warm-water: Centropages hamatus, Temora longicornis, Acartia longiremis, and Evadne nordmanni) were tested with regard to the annual pattern of the water temperature using the dataset of 50-year-long monitoring in the White Sea (1961–2010). The hydrological summer duration increased by 20 days during the last 50 years, as it has been tracked by an earlier warming up of 0–10-m water layer in spring. Calanus glacialis responded to these changes by the appearance of CI copepodites earlier in the season. We suggest that the earlier start and longer period of ice melt may cause a longer phytoplankton bloom and thus may promote better trophic conditions during the period of Calanus reproduction and its early development. In contrast to cold-water C. glacialis, the phenology and abundance of warm-water copepods have not changed significantly. Both the timings of autumn cooling and average summer temperature remained relatively stable since the beginning of observations resulting in steady conditions during the reproductive period of warm-water species. Prolongation of summer had no effect on their reproduction.     

Plakophilins—hard work in the desmosome,recreation in the nucleus?

The linkage of the different types of cytoskeletal proteins to cell adhesion structures at the cytoplasmic membrane and the connection of these contact sites to corresponding sites of adjacent cells is a prerequisite for integrity and stability of cells and tissues. The structurally most prominent types of such cell-cell adhesion complexes are the desmosomes (maculae adhaerentes), which are found in all epithelia and certain non-epithelial tissues. As an element of the cytoskeleton, intermediate filaments are connected to the adhesive desmosomal transmembrane proteins by the cytoplasmic desmosomal plaque proteins. At least three different types of proteins are found in the desmosomal plaque, one of which is represented by the plakophilins, a recently described sub-family of sequence-related armadillo-repeat proteins. Consisting of three isoforms, plakophilins (plakophilin 1 to 3, PKP 1 to 3) are located in all desmosomes in a differentiation-dependent manner. While PKP 2 and PKP 3 are part of almost all desmosome-bearing cell types (PKP 2 except for differentiated cells of stratified epithelia and PKP 3 for hepatocytes and cardiomyocytes), PKP 1 is restricted to desmosomes of cells of stratified and complex epithelia. Besides the architectural function that plakophilins seem to fulfill in the desmosomes, at least PKP 1 and 2 are also localized in the nucleus independently of any differentiation-related processes and with an up to now enigmatic function in this compartment. In the following article we want to summarize the current knowledge concerning structure, function and regulation of the plakophilins that has been achieved during the last decade.