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.

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.

Book Review: Barbujani, G. Come eravamo. Storie dalla grande storia dell’uomo; Laterza: Roma-Bari, Italy, 2022; ISBN: 9788858148785

From Olive Branch to Olive Tree—Global Green Demilitarization and Ecological Civilization

In 2007, a report to the 17th National People’s Congress in Beijing introduced the concept of Ecological Civilization (EC) (Shēngtài Wénmíng 生态文明) to the official lexicon of the Chinese Communist Party (CCP). With origins in the state discourse of the Soviet Union of the 1980s, the term gained new forms of traction in China and abroad as it drew from ecological Marxism, constructive postmodernism, and process philosophy to propose a new technic of statecraft and international cooperation for the development of long-term, global ecological justice and sustainability. In 2012, the constitution of the People’s Republic of China enshrined the goals of EC as a primary national objective, promulgating specific policies on environmental management, green technology, and ideological development. Although some critics view EC discourse as the epitome of authoritarian environmentalism, others cite the PRC’s remarkable strides in developing green technologies and assuming leadership in international treaty negotiations, such as the COP 15, as evidence that the CCP is taking on a new role in global environmental leadership. Beyond the immediate concerns of EC’s performative dimensions, rigorous analysis of EC as a discursive political strategy is critical for understanding its potential for opening spaces of unprecedented international cooperation on planetary environmental governance. While skepticism is in order, facile reductions of the scope of Shēngtài Wénmíng discourse to mere propaganda designed to disguise authoritarian environmentalism marks a dangerous foreclosure on what could very well emerge as a workable vision of international cooperation to solve ecological and social crises arising from the global climate emergency, the Sixth Mass Extinction, and severe regional disparities in resource access. Strong EC theory and practice ascribe transcendent value to the earth’s biogeochemical systems as the very oikos (οίκος)—the ecological home within which human economy and infrastructure engage with more-than-human forces constitutive of “nature” to co-create our shared terrestrial world. Within this highly variegated terrestrial ecology, with its multiplicity of biomes, human and more-than-human potentials can be realized for mutual benefit—the essential condition for sustainability. Given these considerations, to dismiss PE discourse in summary fashion constitutes a grave mistake and an act of bad faith. This analysis reconceptualizes the oikos as deeply similar to the East Asian philosophical concept of Tiānxià (天下) and, concomitantly, equates the Western conception of cosmos (σύμπαν) with the Daoist and Confucian concept of (Tiān天).This vision of wealth and common property embodied in the global biospheric commons grounds, reproduces, and inflects the human terrestrial condition. The mechanism for achieving global EC involves the overcoming of the fundamental contradictions between classical paradigms of industrial development and emerging conceptions of ecological resilience, by fast-tracking ecological development at all terrestrial scales on a foundation of unprecedented international cooperation and social justice. This includes the treatment of scarce mineral resources, which are required to meet the growing global demand for green technologies and mitigate the disastrous effects of global climate change, as common pool resources. EC comprises a radical and crucial reconfiguration of geopolitical theory and practice based on a new ecological ethics for the Anthropocene Epoch. This readjustment of international relations to meet actually existing global crises cannot be realized without a concomitant and symmetrical system of demilitarization based on the transfer of resources, materiel, personnel, expertise, and security policy out of the global military-industrial complex, which centers on monocentric geographic realms (East Asia, North America, the EU, South Asia, and Russia) and a series of shifting alliances the G-7, NATO, the UN. The United States and China currently enjoy an unprecedented degree of prominence and agency on the world stage. They must, for that very reason, play leading roles in global demilitarization. The most effective means of insuring multilateral involvement in this process, and the protocol with the largest peace dividends, is called Global Green Demilitarization. This article provides the philosophical, ethical, and political groundwork to replace destructive practices of resource competition with diplomatic processes leading to international, multilateral, and global Ecological Civilization. The road will be long and perhaps the way will be arduous, but the rewards will exceed the difficulties, consisting, as they will, of a thriving planet and a dynamic, peaceful, and equitable civilization in the 21st century and for the remainder of the third millennium.

Translational Studies Reveal the Divergent Effects of Simtuzumab Targeting LOXL2 in Idiopathic Pulmonary Fibrosis

The composition of extracellular matrix (ECM) is altered during pathologic scarring in damaged organs including the lung. One major change in the ECM involves the cross-linking of collagen, which promotes fibroblast to myofibroblast differentiation. We examined the role of lysyl oxidase (LOX)-like 2 in lung progenitors and fibroblasts cultured from normal or IPF lung samples and in a humanized mouse model of IPF using a monoclonal antibody (Simtuzumab). Primary lung fibroblasts from normal donor lungs and IPF lung explants were examined for expression of LOXL2. Targeting LOXL2 with Simtuzumab on normal and IPF fibroblasts was examined both in vitro and in vivo for synthetic, functional, and profibrotic properties. LOXL2 was increased at transcript and protein level in IPF compared with normal lung samples. In a dose-dependent manner, Simtuzumab enhanced differentiation of fibroblasts into myofibroblasts. Inhibition of LOXL2 also enhanced fibroblast invasion and accelerated the outgrowth of fibroblasts from dissociated human lung cell preparations. Finally, preventative or delayed delivery of Simtuzumab enhanced lung fibrosis in a humanized mouse model of pulmonary fibrosis. Consistent with its failure in a Phase 2 clinical trial, Simtuzumab exhibited no therapeutic efficacy in translational in vitro and in vivo assays.

Enhancing the Monitoring Protocols of Intermittent Flow Rivers with UAV-Based Optical Methods to Estimate the River Flow and Evaluate Their Environmental Status

Temporary streams are a key component of the hydrological cycle in arid and semi-arid regions, but their flow is highly variable and difficult to measure. In this paper, we present a novel approach that could be used to assess the flow of temporary streams this allowing to characterize their environmental status. Specifically, we apply the Image Velocimetry (IV) method to estimate surface velocity in temporary streams using Unmanned Aerial Vehicles (UAVs) equipped with optical sensors (IV-UAV method). The IV-UAV method enables the easy, safe and quick estimation of the velocity on the water’s surface. This method was applied in different temporary streams in Lesvos Island, Greece. The results obtained indicate that the IV-UAV can be implemented at low discharges, temporary streams and small streams. Specifically, the water depth ranged from 0.02 m to 0.28 m, while the channel width ranged from 0.6 m to 4.0 m. The estimated surface velocity ranged from 0.0 to 5.5 m/s; thus, the maximum water discharge was 0.60 m³/s for the largest monitored stream of the island. However, there were many occasions that measurements were unable due to various reasons such as dense vegetation or archaeological sites. Despite of this, the proposed methodology could be incorporated in optical protocols which are used to assess the environmental status of temporary streams of Mediterranean conditions. Finally, this would become a valuable tool for understanding the dynamics of these ecosystems and monitoring changes over time.