A Perspective in Future Biomanufacturing: Challenges in Industrial Fermentation—Understanding and Controlling Microbial Lifespan and Aging

Deciphering the Code of Pattern Formation: Integrating In Silico and Wet Lab Approaches in Synthetic Biology

Pattern formation is a fundamental process in biological development, enabling the transformation of initially uniform or random states into spatially ordered structures. A comprehensive understanding of the formation and function of these patterns is crucial for unraveling the underlying principles of biological design and engineering. In recent years, synthetic biology has emerged as a powerful discipline for investigating and manipulating pattern formation in biological systems, involving the design and construction of novel biological components, circuits, and networks with specific functionalities. The integration of computational simulations (in silico) and experimental techniques (wet lab) in synthetic biology has significantly advanced our knowledge of pattern formation and its implications in biological design and engineering. This review provides an overview of the computational simulations employed in studying pattern formation and introduces the representative and cutting-edge experimental methods utilized in wet labs.

The Infrastructure of an Ecological Civilization Cultivates Stewardship and Safety

TANGO1 Dances to Export of Procollagen from the Endoplasmic Reticulum

The endoplasmic reticulum (ER) to Golgi secretory pathway is an elegantly complex process whereby protein cargoes are manufactured, folded, and distributed from the ER to the cisternal layers of the Golgi stack before they are delivered to their final destinations. The export of large bulky cargoes such as procollagen and its trafficking to the Golgi is a sophisticated mechanism requiring TANGO1 (Transport ANd Golgi Organization protein 1. It is also called MIA3 (Melanoma Inhibitory Activity protein 3). TANGO1 has two prominent isoforms, TANGO1-Long and TANGO1-Short, and each isoform has specific functions. On the luminal side, TANGO1-Long has an HSP47 recruitment domain and uses this protein to collect collagen. It can also tether its paralog isoforms cTAGE5 and TALI and along with these proteins enlarges the vesicle to accommodate procollagen. Recent studies show that TANGO1-Long combines retrograde membrane flow with anterograde cargo transport. This complex mechanism is highly activated in fibrosis and promotes the excessive deposition of collagen in the tissues. The therapeutic targeting of TANGO1 may prove successful in the control of fibrotic disorders. This review focuses on TANGO1 and its complex interaction with other procollagen export factors that modulate increased vesicle size to accommodate the export of procollagen. 

Serine Integrase-based Recombination Enables Direct Plasmid Assembly In Vivo

Serine integrases are emerging as one of the powerful tools for synthetic biology. They have been widely developed across genome engineering, biological part construction, genetic circuit design, and in vitro DNA assembly. However, the strategy of in vivo DNA assembly by serine integrases has not yet been reported. To address this opportunity, here we developed a serine integrase-based in vivo DNA (plasmid) assembly approach. First, we demonstrated that the engineered “Acceptor” plasmids could be assembled with diverse “Donor” plasmids by serine integrases (Bxb1 and phiC31) in Escherichia coli (E. coli). Then, by programming the “Donor” plasmids and the host E. coli cells, we established an assembly cascade procedure and finally constructed plasmids that could constitutively express three different fluorescent proteins. Moreover, we used this approach to assemble different chromoprotein genes and generated colored E. coli cells. We anticipate that this approach will enrich the serine integrase-based biotechnology toolbox, and accelerate multiple plasmid assembly for synthetic biology with broad applications.

Globalization, Urbanization and Rural Transformation

Time-efficient and Semi-automated Production and Screening of Proteins

Fast, flexible and non-randomized modification, production and screening of proteins in fully automated system are of high interest in biological research and applications. The conventional methods for protein engineering and screening, especially for mutations of multiple residues. are time consuming and often unreliable. We demonstrate here a new, fast and flexible protein production and screening method which combines linear expression template (LET) based cell free protein synthesis (CFPS) with specific screening methods. This approach is demonstrated using green fluorescence protein, phosphoserine aminotransferase (serC) and aspartokinase III (AKIII) as model systems. The results show that mutants with changes in different protein properties upon multiple point mutations can be produced and screened within 6 to 15 h. This method can be used further to generate mutants of enzymes and multi-enzyme complexes and be implemented within the workflow of a feedback-guided protein optimization and screening system.

Measurement of Energy Poverty and Influencing Factors of Rural Households in China

Despite being the world’s largest developing country, China faces significant disparities between urban and rural areas, which exacerbates energy poverty in rural regions. This issue of energy poverty is a global concern, as millions of people lack access to modern energy necessary for a decent quality of life. This research aims to analyze the levels and structures of energy consumption in rural Chinese households, using data from the Chinese General Social Survey (CGSS) conducted in 2015 and 2018. The research employs the poverty line threshold and Theil index methods to comprehensively assess energy poverty in diverse regions. It also examines the economic, social, and familial factors influencing rural energy poverty. The findings reveal a transition in rural energy consumption towards cleaner sources, but energy poverty remains a significant issue. Factors such as energy prices and household size have a positive impact on energy poverty, while per capita income, education level, and social factors exert a negative influence. 

The Role of Liability Regime in Addressing Historical Contaminated Land Problems: A Comparative Perspective from England and China

This article conducts a comparative analysis of contaminated land regimes in China and England, focusing on their development, liability attribution, key principles, administrative nature, and financial guarantees. Both regimes are risk-based and are supported by the Polluter Pays Principle and the Stewardship Principle. They have similar liability arrangements: attributing the liability firstly to the polluter and then to landowners/occupiers or the usufructuaries. Administrative authorities under both regimes hold pivotal roles in remediating land on certain occasions. However, the cost recovery mechanisms vary due to the different constitutional roles among enforcing authorities, courts, and liable parties in the two countries. Both regimes impose retrospective liability, yet England provides detailed rules regarding the hardship provision and exclusion tests, preventing the unfair allocation of liability more effectively. Experience from England highlights the limited role of legal regimes in managing historical pollution, emphasising the need for supplementary mechanisms. This is why financial support is critical for effective land remediation in both countries. 

Have We Been Barking up the Wrong Ancestral Tree? Australopithecines Are Probably Not Our Ancestors

The dominant paradigm regarding human evolution since the split with Pan considers australopithecines as hominins, i.e., the closest relatives and/or direct ancestors of Homo. Historically, this paradigm started from the assumption that the Homo/Pan/Gorilla last common ancestor was a knuckle-walking ape that evolved into the fully upright (orthograde), obligate bipedal genus Homo, whereas Pan and Gorilla remained knuckle-walkers. Obligate terrestrial upright bipedalism, unique for our species, is an odd locomotor behaviour for a primate. Therefore, it had become generally accepted that a cooler and drier African climate had caused deforestation, which had forced our ancestors to develop upright bipedalism as an adaptation to living on open grassland savannah. This view, already held by Lamarck and Darwin, appeared most parsimonious in the almost complete absence of fossils. The discovery in the 20th century of australopithecine fossils, bipedal apes with small brains, in open country in southern and eastern Africa corroborated the savannah paradigm. Therefore, australopithecines are considered hominins. However, it is now recognized that most australopithecines instead lived in a mosaic of forests, grasslands and wetlands, and better knowledge of their fossils clearly indicates that they possessed several climbing adaptations. Moreover, none of the extinct ape species older than Australopithecus and Paranthropus for which postcranial remains have been described (e.g., Morotopithecus, Sahelanthropus, Orrorin, Ardipithecus) were knuckle-walking. On the other hand, upright posture/gait is already present to different degrees even in Miocene apes. Moreover, the notion that hominoid orthogrady is a primitive characteristic is corroborated by the growing consensus that knuckle-walking is not a primitive trait but has evolved in parallel, independently in both Pan and Gorilla. Consequently, it is possible that australopithecines are not transitional between a semi-erect ancestor and upright bipedal humans, but to the contrary, are intermediate between a more upright ancestor and extant semi-erect African apes. In summary, hypotheses that attempt to explain how a semi-erect Homo/Pan last common ancestor transitioned into the bipedal australopithecines as an adaptation to life on the savannah appear to be ill-conceived and moreover seem to have been superfluous from the very start. We review the numerous similarities between australopithecines and extant African apes, suggesting that they are possibly not hominins and therefore not our direct ancestors. We suggest that we may have been barking up the wrong ancestral tree, for almost a century.