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The bookshelf behind my writing desk is overburdened with heavy tomes about classical Greece and Rome. It teeters with biographies of Caesar, Hannibal, Scipio Africanus, Cato, and Seneca. There are works by Pliny the Elder, Apuleius, Epicurus, and Gibbon. There are books filled with maps, charts, and case studies on famous battles.
I got these books during college, in Iowa City. Some were bought for pennies, from hidden and used bookstores. For the others, I gambled, swindled, bargained, and traded into their possession. My tactics may seem strange, but Iowa City is a strange place, filled with book obsessives who spend their evenings at writing desks. It felt normal, there and then, to amass thousands of books but live an otherwise Spartan lifestyle.
Iowa City is also the place where I first fell in love with classical history. In my four years, and with scant time for electives, I somehow managed to take six courses in Roman and Greek history.
In reading about Rome, my brain went on holiday. Reading Gibbon felt much like watching an ancient soap opera. The never-ending wars, poisonings, and mock naval battles (after gladiatorial games become passé) are exciting enough to suck in most people with an appetite for adventure. I consumed books at a prodigious pace. One time, I sat for a graduate-level, multiple-choice exam (I think the course was about the Severan dynasty) and finished in ten minutes with a perfect score. A few days later, at a non-optional meeting with the professor, I had to explain that I hadn’t cheated — I was just obsessed with Roman history.
So why am I telling you this? It’s because I’ve been writing this newsletter for years, and there’s finally a paper that perfectly melds my fragmented love for history and genetics. In it, a broad coalition of researchers — from Harvard, Florence, Lecce, and elsewhere — explain how they sequenced and analyzed genetic information from 54 Greek soldiers who lived in Sicily between the eighth- and fifth centuries B.C.
Their results suggest that European wars, more than 2,500 years ago, displaced people and moved them hundreds or thousands of miles to serve under the wills of kings and rulers in faraway lands. Rulers enlisted both local people and mercenaries to fight wars. Armies were remarkably diverse. These mercenaries (or, perhaps, slaves?) came from distant lands in northern Europe and modern-day Azerbaijan. Somehow, they all ended up in Sicily, in a town called Himera, near the edge of their world.
The western coast of Sicily was settled by the Phoenicians (modern-day Lebanon) as a trading post as early as the ninth century B.C. They sailed from Asia across the Mediterranean, and encountered local, Iron Age ethnic groups upon landing in Sicily.
A hundred years later, the Greeks came. The town of Himera was founded and built by the Ionian and Dorian Greeks, from present-day Turkey and Crete, respectively. But the town was multicultural. It bustled and swarmed with thousands of indigenous Sicilians and Etruscans.
In 480 B.C. and 409 B.C., two battles wracked Himera’s shores. Greeks fought against Carthaginians. Thousands died. Sicily won the first battle but lost the second. The island soon fell. The bodies of soldiers were buried in a mass grave to the west of town.
And it is here, nearly two millennia and 500 years later, that our story begins.
Archaeologists and geneticists swoop in and take DNA samples “from 33 individuals associated with the Battles of Himera and from Himera’s civilian population, as well as 21 individuals from two nearby settlements” — the Iron Age sites of Polizzello and Monte Falcone at Baucina — “associated with the indigenous Sicani culture of Sicily.” Their goal is to find out who lived, breathed, and fought in these places, and to pinpoint their ancestral origins.
All the soldiers were men, while five of the indigenous Sicani were women. Genetic data were compared to DNA collected from 96 modern-day Italians, Greeks, and Cretans.
Many of the soldiers, in both battles, had genetic data which resembled those of modern-day Greeks. These soldiers were probably inhabitants of Himera and were conscripted to fight in the wars against Carthage. Others likely came from supporting outposts in Syracuse. Most of the soldiers were probably “descendants of the Greek colonizers of Sicily,” who married and had children with the local Sicilians.
But nine soldiers who fought in the battle of 480 B.C. didn’t fit this mold. Their genetic data stood out; it was different.
One soldier likely came from the Balkans, while two came from northeastern Europe (probably Lithuania), and two were descended from nomadic peoples — the Han or Karitiana natives — who roamed the Eurasian Steppes. One soldier’s mitochondrial DNA resembled those of people in modern-day China, while another’s resembled people from modern-day Russia, Kazakhstan, or Mongolia.
These soldiers, then, were probably mercenaries. And this finding is bolstered by strontium and oxygen isotope data. These isotopic ratios reflect where a person lived while their teeth and bones developed, and can provide valuable clues into where a person moved and traveled during their life.
A low oxygen ratio is “characteristic of higher latitudes, higher altitudes, cooler climates, greater rainfall, and greater distances from coasts than Himera,” while a higher strontium ratio indicates “more ancient underlying rocks and soils” than those present at Himera. These ratios were consistent with the genetic information.
Diodorus Siculus, a historian from Sicily who lived in the 1st century B.C., never mentioned the presence of mercenaries in Himera in 480 B.C. But he did mention that a Syracusan tyrant, named Gelon, “had gathered a large number of foreign mercenaries to round out his army” sometime prior. It’s likely that these are the mercenaries who helped push back the Carthaginian force in that initial battle in 480 B.C.
It’s no surprise that Greece enlisted mercenaries. Punic armies, including Carthage, did the same. But what is amazing about these genetic data is that they tell the story about why Himera fell in 409 B.C.
It fell because Greece never sent reinforcements or mercenaries. DNA from soldiers of the second battle suggest only ancestral origins in modern-day Sicily and Greece. The town and its people were left to fend for themselves. Gone were the mercenaries from northeastern Europe. Gone were the soldiers from the Eurasian Steppes. Gone were the Greek mercenaries amidst the surging threat of a Carthaginian invasion.
Greece left Hemira to perish.
P.S. For more stuff like this, I recommend reading David Reich’s book, Who We Are and How We Got Here.
Thanks for reading,
— Niko McCarty
Synthetic Biology Index
(↑ = recommended article, * = open access, † = review, comment, etc. )
*Integrative dissection of gene regulatory elements at base resolution. Chen Z…Bernstein BE. bioRxiv (preprint). Link
*Engineering Nanowires in Bacteria to Elucidate Electron Transport Structural Functional Relationships. Myers B…Rawson F. bioRxiv (preprint). Link
↑*Systematic dissection of key factors governing recombination outcomes by GCE-SCRaMbLE. Zhang H…Shen Y. Nature Communications. Link
*Molecular mechanism of active Cas7-11 in processing CRISPR RNA and interfering target RNA. Goswami HN…Li H. eLife. Link
*Capsid-mediated chromatin state of the AAV vector genome controls host species range. Gonzalez-Sandoval A…Kay MA. bioRxiv (preprint). Link
Biomanufacturing & Metabolic Engineering
↑*Predictive evolution of metabolic phenotypes using model-designed environments. Jouhten P…Patil KR. Molecular Systems Biology. Link
↑Spatial engineering of E. coli with addressable phase-separated RNAs. Guo H…Lindner AB. Cell. Link
- An amazing paper, which I didn’t see last week. In E. coli, RNA-binding proteins attach to CAG repeats in RNA sequences. This causes liquid-liquid phase separation in the cytoplasm. And this simple technology can be used to spatially separate the translation of key proteins in metabolic pathways from one another! Surely a useful tool for metabolic engineering.
†*Prospects for carbon-negative biomanufacturing. Scown CD. Trends in Biotechnology. Link
†Micro-aeration: an attractive strategy to facilitate anaerobic digestion. Fu S…Guo R. Trends in Biotechnology. Link
†Microalgae-based biotechnological sequestration of carbon dioxide for net zero emissions. Ma Z…Show PL. Trends in Biotechnology. Link
*Engineering Escherichia coli to utilize erythritol as sole carbon source. Ba F…Li J. bioRxiv (preprint). Link
*Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models. Wilken SE…Ebenhöh O. Metabolic Engineering. Link
Control of Enzyme Reaction Initiation inside Giant Unilamellar Vesicles by the Cell-Penetrating Peptide-Mediated Translocation of Cargo Proteins. Miwa A & Kamiya K. ACS Synthetic Biology. Link
*Production of biopolymer precursors beta-alanine and L-lactic acid from CO2 with metabolically versatile Rhodococcus opacus DSM 43205. Salusjärvi L…Toivari M. Frontiers in Bioengineering and Biotechnology. Link
†Applications of bio-capacitance to cell culture manufacturing. Bergin A, Carvell J & Butler M. Biotechnology Advances. Link
Metabolic Engineering Mevalonate Pathway Mediated by RNA Scaffolds for Mevalonate and Isoprene Production in Escherichia coli. Liu C-L…Tan T-W. ACS Synthetic Biology. Link
Building an Artificial Plant Cell Wall on a Lipid Bilayer by Assembling Polysaccharides and Engineered Proteins. Notova S…Imberty A. ACS Synthetic Biology. Link
↑*Orthogonal tRNA Expression using Endogenous Machinery in Cell-Free Systems. Seki K, Galindo JL & Jewett MC. bioRxiv (preprint). Link
- A new cell-free system can be used to rapidly test orthogonal tRNAs to make proteins with an expanded repertoire of amino acids. This technology was used to simultaneously express two such tRNAs (both TAG- and TAA-suppressing) to make a protein with two added, noncanonical amino acids.
↑*SpyPhage: A Cell-Free TXTL Platform for Rapid Engineering of Targeted Phage Therapies. Liyanagedera SBW…Kulkarni V. ACS Synthetic Biology. Link
*Characterization of Integrase and Excisionase Activity in Cell-free Protein Expression System Using a Modeling and Analysis Pipeline. Pandey A…Murray RM. bioRxiv (preprint). Link
*Cell-free protein crystallization for nanocrystal structure determination. Abe S…Ueno T. Scientific Reports. Link
Computational Tools & Models
↑Single-sequence protein structure prediction using a language model and deep learning. Chowdhury R…AlQuraishi M. Nature Biotechnology. Link
BIONIC: biological network integration using convolutions. Forster DT…Boone C. Nature Methods. Link
*RNA secondary structure packages evaluated and improved by high-throughput experiments. Wayment-Steele HK…Das R. Nature Methods. Link
Comprehensive transcription terminator atlas for Bacillus subtilis. Mandell ZF…Babitzke P. Nature Microbiology. Link
*TFSyntax: a database of transcription factors binding syntax in mammalian genomes. Zhao Y. Nucleic Acids Research. Link
*SoloTE for improved analysis of transposable elements in single-cell RNA-Seq data using locus-specific expression. Rodríguez-Quiroz R & Valdebenito-Maturana B. Communications Biology. Link
*EURISCO update 2023: the European Search Catalogue for Plant Genetic Resources, a pillar for documentation of genebank material. Kotni P…Weise S. Nucleic Acids Research. Link
CRISPR, Gene Editing & Control
↑Precise DNA cleavage using CRISPR-SpRYgests. Christie KA…Kleinstiver BP. Nature Biotechnology. Link
- An engineered Cas9 protein, called SpRY, “is PAMless in vitro and can cleave DNA at practically any sequence.” That’s amazing, and it should expand the repertoire of genetic edits available in cell-free systems, for example, or for CRISPR-based diagnostics.
Enzyme-free targeted DNA demethylation using CRISPR–dCas9-based steric hindrance to identify DNA methylation marks causal to altered gene expression. Sapozhnikov DM & Szyf M. Nature Protocols. Link
*Marker-free co-selection for successive rounds of prime editing in human cells. Levesque S…Doyon Y. Nature Communications. Link
†CRISPR-Cas13 technology portfolio and alliance with other genetic tools. Wu S, Tian P & Tan T. Biotechnology Advances. Link
*Efficient Bacterial Genome Engineering throughout the Central Dogma Using the Dual-Selection Marker tetA(OPT). Bayer CN…Nørholm MHH. ACS Synthetic Biology. Link
DNA Sequencing, Synthesis & Assembly
↑*Design, Construction, and Functional Characterization of a tRNA Neochromosome in Yeast. Schindler D…Cai Y. bioRxiv (preprint). Link
- This paper is a long time coming. The Sc2.0 project was first proposed in the mid-2000s. The goal, then as now, is to build the first eukaryotic genome completely from scratch. Baker’s yeast, Saccharomyces cerevisiae, was the obvious choice.
As part of that project, the Sc2.0 team decided to move all of the genes encoding tRNAs to a standalone chromosome. This new chromosome would house all 275 of these genes, and include slightly more than 190,000 base pairs of DNA. Once complete, the chromosome would vastly simplify efforts to expand the genome of Baker’s yeast, or to manufacture proteins with added, noncanonical amino acids.
And now it’s done. The neochromosome, though, added quite a lot of “burden” to the yeast cells and is generally unstable. Still, it’s an amazing accomplishment that lends powerful insights for those bioengineers hoping to write new genomes. Indeed, this is the only chromosome in the Sc2.0 project that was not based on a natural chromosome template. It was literally designed and created from scratch, sequence and all.
↑*Reconstruct a eukaryotic chromosome arm by de novo design and synthesis. Jiang S…Dai J. bioRxiv (preprint). Link
*A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome. Keraite I…Gut IG. Nature Communications. Link
↑*Control of spatio-temporal patterning via cell density in a multicellular synthetic gene circuit. Santorelli M…Morsut L. bioRxiv (preprint). Link
↑*Highly-Automated, High-Throughput replication of yeast-based logic circuit design assessments. Goldman RP…Colonna-Romano J. Synthetic Biology. Link
- An important paper shows that cloud labs (specifically, Strateos) can be used to quickly build and test genetic circuits in yeast at high throughput. Robotics will prove increasingly important for synthetic biology, especially for testing engineered strains and replicating results.
Modular, Synthetic Boolean Logic Gates Enabled in Saccharomyces cerevisiae through T7 Polymerases/CRISPR dCas9 Designs. Presnell KV…Alper HS. ACS Synthetic Biology. Link
Medicine & Diagnostics
*Development of intravenously administered synthetic RNA virus immunotherapy for the treatment of cancer. Kennedy EM…Lerner L. Nature Communications. Link
*Pancreatic islet-specific engineered Tregs exhibit robust antigen-specific and bystander immune suppression in type 1 diabetes models. Yang SJ…Buckner JH. Science Translational Medicine. Link
*Combating the SARS-CoV-2 Omicron (BA.1) and BA.2 with potent bispecific antibodies engineered from non-Omicron neutralizing antibodies. Wang Y…Huang J. Cell Discovery. Link
*IgG-like bispecific antibodies with potent and synergistic neutralization against circulating SARS-CoV-2 variants of concern. Chang MR…Marasco WA. Nature Communications. Link
*DNA-delivered antibody cocktail exhibits improved pharmacokinetics and confers prophylactic protection against SARS-CoV-2. Parzych EM…Weiner DB. Nature Communications. Link
*Chemical engineering of therapeutic siRNAs for allele-specific gene silencing in Huntington’s disease models. Conroy F…Pfister EL. Nature Communications. Link
*Novel triplex nucleic acid lateral flow immuno-assay (NALFIA) for rapid detection of Nipah virus, Middle East respiratory syndrome coronavirus and Reston ebolavirus. Chingtham S…Raut AA. bioRxiv (preprint). Link
*A bivalent SARS-CoV-2 monoclonal antibody combination does not affect the immunogenicity of a vector-based COVID-19 vaccine in macaques. Nkolola JP…Barouch DH. Science Translational Medicine. Link
Detection of target DNA with a visual CRISPR-associated hyperbranched rolling circle amplification technique. Zhang B…Song Z. Analytical Biochemistry. Link
†Cybergenetic control of microbial community composition. Lee TA & Steel H. Frontiers in Bioengineering and Biotechnology. Link
*Expression strategies for the efficient synthesis of antimicrobial peptides in plastids. Hoelscher MP…Bock R. Nature Communications. Link
*Abatement of Microfiber Pollution and Detoxification of Textile Dye – Indigo by engineered plant enzymes. Wakade G…Daniell H. Plant Biotechnology Journal. Link
*Functional expression of the nitrogenase Fe protein in transgenic rice. Baysal C…Christou P. Communications Biology. Link
†The cost of not adopting new agricultural food biotechnologies. Paarlberg R & Smyth SJ. Trends in Biotechnology. Link
Tissue, Protein & Molecular Engineering
↑*De novo design of immunoglobulin-like domains. Chidyausiku TM…Marcos E. Nature Communications. Link
NMR-guided directed evolution. Bhattacharya S…Korendovych IV. Nature. Link
Dissecting the stability determinants of a challenging de novo protein fold using massively parallel design and experimentation. Kim T-E…Rocklin GJ. PNAS. Link
Tools & Technology
↑Programmable RNA sensing for cell monitoring and manipulation. Qian Y…Huang ZJ. Nature. Link
↑Modular, programmable RNA sensing using ADAR editing in living cells. Kaseniit KE…Gao XJ. Nature Biotechnology. Link
- Both of the above papers have gotten a lot of attention, and deservedly so. They report tools that can be used to sense a broad range of RNA sequences inside living cells, using a type of protein called an adenosine deaminase. I’ll write more about this soon.
Genetically encoded chemical crosslinking of RNA in vivo. Sun W…Wang L. Nature Chemistry. Link
*Engineering Endosymbiotic Growth of E. coli in Mammalian Cells. Gäbelein CG…Vorholt JA. ACS Synthetic Biology. Link
Evaluation of Human Performance Aiding Live Synthetically Engineered Bacteria in a Gut-on-a-Chip. Nelson MT…Mauzy CA. ACS Biomaterials Science & Engineering. Link
*Accurate characterization of dynamic microbial gene expression and growth rate profiles. Vidal G…Rudge TJ. Synthetic Biology. Link
*Attogram-level light-induced antigen-antibody binding confined in microflow. Iida T…Tokonami S. Communications Biology. Link
*Rapid quantification of miRNAs using dynamic FRET-FISH. Kim J…Hohng S. Communications Biology. Link
High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging. He S…Beechem JM. Nature Biotechnology. Link
Other Interesting Stuff
*A brain atlas of synapse protein lifetime across the mouse lifespan. Bulovaite E…Grant SGN. Neuron. Link
†Defending Earth’s terrestrial microbiome. Averill C…Crowther TW. Nature Microbiology. Link
*Nuclear-embedded mitochondrial DNA sequences in 66,083 human genomes. Wei W…Chinnery PF. Nature. Link
*Nobel and novice: Author prominence affects peer review. Huber J…Smith VL. PNAS. Link
*The diverse genetic origins of a Classical period Greek army. Reitsema LJ…Reich D. PNAS. Link
*Past and present giant viruses diversity explored through permafrost metagenomics. Rigou S…Legendre M. Nature Communications. Link
*Environmental complexity is more important than mutation in driving the evolution of latent novel traits in E. coli. Karve S & Wagner A. Nature Communications. Link