Biomedical subjects

Han Zhu

Publications and source records attributed to Han Zhu.

7 recordsLinked to original sources

PubMed2025

Epitranscriptomic reprogramming in response to low CO2 stress and m6A engineering to enhance biomass production in Nannochloropsis oceanica.

N6-adenine methylation (m6A) as an epitranscriptomic mark is the most abundant modification in eukaryotic RNA and plays a dynamically regulated role. However, m6A dynamics, deposition and engineering in microalgae remain largely unknown. Here, in Nannochloropsis oceanica, the dynamic alterations and reprogramming in m6A RNA modifications after the shift from high to low CO2 conditions were first investigated using methylated RNA immunoprecipitation sequencing. The m6A peaks in N. oceanica were mainly enriched in 3'UTR. A positive association between m6A abundance and mRNA transcription of CO2-responsive genes was observed; moreover, N. oceanica cells adopted versatile strategies in a dynamic reprogramming of m6A in response to low CO2 stress. Secondly, knockout of two putative m6A methylases including NoMTA (NO04G02990) and NoMTB (NO07G02450) by genome editing induced methylation reprogramming, which was associated with expression changes of low-CO2 responsive genes such as carbon/nitrogen metabolism, and photorespiration genes that underlie reductions in growth and biomass. Lastly, m6A modification reprogramming was first engineered to increase low-CO2 stress tolerance and biomass productivity by the CRISPR/dCas13 system combined with MTA and NoMTB under low CO2 in N. oceanica. Therefore, these strides would pave the way for microalgal epigenetics and future industrial applications.

Microalgae↗

PubMed2004

Navigation in a small world with local information.

It is commonly known that there exist short paths between vertices in a network showing the small-world effect. Yet vertices, for example, the individuals living in society, usually are not able to find the shortest paths, due to the very serious limit of information. To study this issue theoretically, here the navigation process of launching messages toward designated targets is investigated on a variant of the one-dimensional small-world network (SWN). In the network structure considered, the probability of a shortcut falling between a pair of nodes is proportional to r(-alpha) , where r is the lattice distance between the nodes. When alpha=0 , it reduces to the SWN model with random shortcuts. The system shows the dynamic small-world effect, which is different from the well-studied static SW effect. We study the effective network diameter, the path length as a function of the lattice distance, and the dynamics. They are controlled by multiple parameters, and we use data collapse to show that the parameters are correlated. The central finding is that, in the one-dimensional network studied, the dynamic SW effect exists for 0</=alpha</=2 . For each given value of alpha in this region, the point where the dynamic SW effect arises is M L' approximately 1 , where M is the number of useful shortcuts and L' is their average reduced (effective) length.

Journal Article↗

PubMed2003

Effect of aging on network structure.

In network evolution, the effect of aging is universal: in scientific collaboration network, scientists have a finite time span of being active; in movie actors network, once popular stars are retiring from stage; devices on the Internet may become outmoded with techniques developing so rapidly. Here we find in citation networks that this effect can be represented by an exponential decay factor, e(-betatau), where tau is the node age, while other evolving networks (the Internet, for instance) may have different types of aging, for example, a power-law decay factor, which is also studied and compared. It has been found that as soon as such a factor is introduced to the Barabasi-Albert scale-free model, the network will be significantly transformed. The network will be clustered even with infinitely large size, and the clustering coefficient varies greatly with the intensity of the aging effect, i.e., it increases linearly with beta for small values of beta and decays exponentially for large values of beta. At the same time, the aging effect may also result in a hierarchical structure and a disassortative degree-degree correlation. Generally the aging effect will increase the average distance between nodes, but the result depends on the type of the decay factor. The network appears like a one-dimensional chain when exponential decay is chosen, but with power-law decay, a transformation process is observed, i.e., from a small-world network to a hypercubic lattice, and to a one-dimensional chain finally. The disparities observed for different choices of the decay factor, in clustering, average node distance, and probably other aspects not yet identified, are believed to bear significant meaning on empirical data acquisition.

Journal Article↗

PubMed2003

Introducing small-world network effects to critical dynamics.

We analytically investigate the kinetic Gaussian model and the one-dimensional kinetic Ising model of two typical small-world networks (SWN), the adding type and the rewiring type. The general approaches and some basic equations are systematically formulated. The rigorous investigation of the Glauber-type kinetic Gaussian model shows the mean-field-like global influence on the dynamic evolution of the individual spins. Accordingly a simplified method is presented and tested, which is believed to be a good choice for the mean-field transition widely (in fact, without exception so far) observed for SWN. It yields the evolving equation of the Kawasaki-type Gaussian model. In the one-dimensional Ising model, the p dependence of the critical point is analytically obtained and the nonexistence of such a threshold p(c), for a finite-temperature transition, is confirmed. The static critical exponents gamma and beta are in accordance with the results of the recent Monte Carlo simulations, and also with the mean-field critical behavior of the system. We also prove that the SWN effect does not change the dynamic critical exponent z=2 for this model. The observed influence of the long-range randomness on the critical point indicates two obviously different hidden mechanisms.

Journal Article↗

PubMed2002

Generalized competing Glauber-type dynamics and Kawasaki-type dynamics.

In this paper, we have given a systematic formulation of a generalized competing mechanism: The Glauber-type single-spin transition mechanism, with probability p, simulates the contact of the system with the heat bath, and the Kawasaki-type spin-pair redistribution mechanism, with probability 1-p, simulates an external energy flux. These two mechanisms are natural generalizations of Glauber's single-spin flipping mechanism and Kawasaki's spin-pair exchange mechanism respectively. On the one hand, the proposed mechanism is, in principle, applicable to arbitrary systems, while on the other hand, our formulation is able to contain a mechanism that just directly combines single-spin flipping and spin-pair exchange in their original form. Compared with the conventional mechanism, the proposed mechanism does not assume the simplified version and leads to a greater influence of temperature. The fact, order for lower temperature and disorder for higher temperature, will be universally true. In order to exemplify this difference, we applied the mechanism to the one-dimensional Ising model and obtained analytical results. We also applied this mechanism to the kinetic Gaussian model and found that above the critical point there will be only paramagnetic phase, while below the critical point, the self-organization as a result of the energy flux will lead the system to an interesting heterophase, instead of the initially guessed antiferromagnetic phase. We studied this process in details.

Journal Article↗

PubMed2002

Kawasaki-type dynamics: diffusion in the kinetic Gaussian model.

In this Brief Report, we retain the basic idea and at the same time generalize Kawasaki's dynamics, the spin-pair exchange mechanism, to a spin-pair redistribution mechanism, and present a normalized redistribution probability. This serves to unite various order-parameter-conserved processes into a universal framework in microscopics and provides the basis for further treatment. As an example of the applications, we treated the kinetic Gaussian model and obtained the exact diffusion equation. We observed critical slowing down near the critical point and found that the critical dynamic exponent z = 1/v = 2 is independent of space dimensionality and the assumed mechanism, whether Glauber type or Kawasaki type.

Journal Article↗

PubMed2002

Adding crumb rubber into exterior wall materials.

In Arizona US, most houses are built with walls covered by stuccos/coatings/mortars. This paper presents an explorative investigation of adding crumb rubber into stuccos/coatings/mortars. A series of experiments are conducted to examine the thermal and mechanical performance of the crumb rubber mixes. The results show that, the mixes with crumb rubber do exhibit more desirable performances like being high in crack-resistance and thermal insulation, and low in thermal expansion/contraction. The drawback for the crumb rubber mixes is the reduction in compressive strength, but which can be compensated by other means. As a site experiment, an area of 100 square-feet of crumb rubber coatings for two mix designs is sprayed on a tire-adobe wall. After being sprayed more than 14 months, the coatings apparently are in good condition. Significance of this study is that this practice, if accepted, will yield improved products that consume large quantities of crumb rubber.

Arizona↗