Question 8: Bridging the Gap Between In Silico and In Vitro Approaches to Minimal Cells

In this short paper we argue for the relevance and value of theoretical models in the field of origins of life, but also claim that both theoreticians and experimentalists should make an effort to come together and interact more closely to obtain more fruitful and significant results. As an example, we present our own modeling approach to protocell dynamics, including some simulation results, to show that it is possible to develop computational tools that start bridging that traditional gap between theory and experiments. Presented at: International School of Complexity – 4th Course: Basic Questions on the Origins of Life; “Ettore Majorana” Foundation and Centre for Scientific Culture, Erice, Italy, 1–6 October 2006.     

中国西南地区的生态危机

一、引言在前所未有的人口激增与经济发展的冲击下,中国的生态环境正经历着巨大的变化。西     

Designing optimal human‐modified landscapes for forest biodiversity conservation

Agriculture and development transform forest ecosystems to human‐modified landscapes. Decades of research in ecology have generated myriad concepts for the appropriate management of these landscapes. Yet, these concepts are often contradictory and apply at different spatial scales, making the design of biodiversity‐friendly landscapes challenging. Here, we combine concepts with empirical support to design optimal landscape scenarios for forest‐dwelling species. The supported concepts indicate that appropriately sized landscapes should contain ≥ 40% forest cover, although higher percentages are likely needed in the tropics. Forest cover should be configured with c. 10% in a very large forest patch, and the remaining 30% in many evenly dispersed smaller patches and semi‐natural treed elements (e.g. vegetation corridors). Importantly, the patches should be embedded in a high‐quality matrix. The proposed landscape scenarios represent an optimal compromise between delivery of goods and services to humans and preserving most forest wildlife, and can therefore guide forest preservation and restoration strategies.     

慢性髓细胞白血病急变期MICM 分型回顾性分析

目的:探讨慢性髓细胞白血病急变期(CML-BC)患者的细胞形态学(M)、免疫学(I)、细胞遗传学(C)和分子生物学(M)的特征及应用价值。方法:对38例CML-BC患者的MICM分型进行回顾性分析。结果:以FAB分型为基础的形态学确诊率达94.7%;免疫分型结果为:38例CML-BC中CML-AML占71.0%,其中37.0%伴淋系表达;CML-ALL占23.7%,均为B细胞性,其中66.67%伴髓系表达;CML-MAL(混合性白血病)占5.3%,均为B系和髓系混合表达;CD34+26例(68.4%),CD7+10例(26.3%),均与CD34共表达。细胞遗传学结果显示:CML特征性Ph染色体检出率为94.3%(36/38),附加异常染色体检出率为60.5%(23/38),发生频率较高的类型是+Ph、+8和i(17q);FISH检测BCR/ABL融合基因阳性率为100%,der(9)缺失占14.7%。RT-PCR检测20例患者BCR/ABL融合基因均为阳性,其中b2a2型(12/20),b3a2型(8/20),1例(1/20),b2a2和b3a2双阳性(1/20)。结论:CML-BC是造血干细胞疾病,原始细胞分化阻滞在早期阶段,预后差。MICM分型对CML-BC的诊断、治疗和预后判断均有重要价值。     

A genetic survey of heavily exploited, endangered turtles: caveats on the conservation value of trade animals

Asian turtles face an extinction crisis, and so it is imperative that systematists accurately determine species diversity in order to guide conservation strategies effectively. We surveyed mitochondrial and nuclear DNA (mtDNA and nuDNA) variation of the heavily exploited Mauremys mutica complex, a clade of Asian turtles that contains the endangered M. mutica from Japan, Taiwan, China and Vietnam, and the critically endangered Mauremys annamensis from central Vietnam. We discovered extensive mtDNA and nuDNA variation among samples that did not correspond to the currently recognized taxonomy. Both nuDNA and mtDNA data suggest that M. mutica is paraphyletic with respect to M. annamensis . Surprisingly, M. annamensis exhibits a previously unknown mtDNA structure in the form of two clades that are paraphyletic to M. mutica . These data reveal that the currently recognized taxonomy of the mutica complex does not reflect the genetic diversity of our samples. Unfortunately, many conservation-oriented captive-breeding efforts for turtles are also based on trade samples such as the ones studied here. These efforts include plans to breed trade-rescued individuals and release their progeny into the wild. Because our genetic survey reveals that the taxonomic identity of these samples does not reflect genetic diversity, we raise serious questions about the efficacy of these programs. In order to address conservation issues and provide more accurate estimates of evolutionary lineages within Mauremys , we recommend continued surveys for wild populations of the mutica complex to provide new genetic material and additional distributional data, attempts to extract DNA from historic museum specimens and a shift in conservation focus to in situ preservation of wild populations and associated habitat.     

Vyazniki biotic assemblage of the terminal Permian

A new unique and diverse biotic assemblage of the terminal Permian has recently been discovered in the town of Vyazniki (Central Russia). The Vyazniki terrestrial community is transitional between Permian and Triassic ones and represents the last, so far unknown stage of the global ecological crisis of the continental biota at the Permian-Triassic boundary. The successive development of land biotic crisis in the Late Permian, which was followed by mass extinction at the Permian-Triassic boundary, and long, successive postcrisis development and specialization of new Triassic groups as well as rearrangement and diversification of the biotic assemblage composition and community structure suggest predominance of intrinsic, biotic causes of this crisis, realized in destabilization, alteration, and new stabilization of continental communities and ecosystems.     

The emergence of the social‐ecological restoration concept

Many ecosystems in the world are the result of a close interaction between local people and their environment, which are currently recognized as social‐ecological systems (SoES). Natural catastrophes or long‐standing social and political turmoil can degrade these SoES to a point where human societies are no longer autonomous and their supporting ecosystems are highly degraded. Here, we focus on the special case of the restoration of SoES that we call social‐ecological restoration (SoER), which is characterized as a restoration process that cannot avoid simultaneously dealing with ecological and social issues. In practice, SoER is analogous in many ways to the general principles of ecological restoration, but it differs in three key aspects: (1) the first actions may be initially intended for human groups that need to recover minimum living standards; (2) the SoER process would often be part of a healing process for local people where cultural values of ecosystems play an essential role; and (3) there is a strong dependency on external economic inputs, as the people belonging to the SoES may be incapable of reorganizing themselves on their own and supporting ecosystems can no longer self‐recover. Although it might not be desirable or necessary to call all restoration projects with a social component an SoER, the use of this concept may help in defining early restoration targets that may prevent conflicts among users in the long term. From the perspective of other disciplines, SoER would be more appropriately perceived as programs of “social‐ecological recovery” in the long term.     

Whiskers-less HIV-protease: a possible way for HIV-1 deactivation

Background

Among viral enzymes, the human HIV-1 protease comprises the most interesting target for drug discovery. There are increasing efforts focused on designing more effective inhibitors for HIV-1 protease in order to prevent viral replication in AIDS patients. The frequent and continuous mutation of HIV-1 protease gene creates a formidable obstacle for enzyme inhibition which could not be overcome by the traditional single drug therapy. Nowadays, in vitro and in silico studies of protease inhibition constitute an advanced field in biological researches. In this article, we tried to simulate protease-substrate complexes in different states; a native state and states with whiskers deleted from one and two subunits. Molecular dynamic simulations were carried out in a cubic box filled with explicit water at 37°C and in 1atomsphere of pressure.

Results

Our results showed that whisker truncation of protease subunits causes the dimer structure to decrease in compactness, disrupts substrate-binding site interactions and changes in flap status simultaneously.

Conclusions

Based on our findings we claim that whisker truncation even when applied to a single subunit, threats dimer association which probably leads to enzyme inactivation. We may postulate that inserting a gene to express truncated protease inside infected cells can interfere with protease dimerization. The resulted proteases would presumably have a combination of native and truncated subunits in their structures which exert no enzyme activities as evidenced by the present work. Our finding may create a new field of research in HIV gene therapy for protease inhibition, circumventing problems of drug resistance.