Lim Ulrich sequences and Boij-S\"{o}derberg cones

This paper extends the results of Boij, Eisenbud, Erman, Schreyer, and S\"oderberg on the structure of Betti cones of finitely generated graded modules and finite free complexes over polynomial rings, to all finitely generated graded rings admitting linear Noether normalizations. The key new input is the existence of lim Ulrich sequences of graded modules over such rings.Comment: 26 page

Structural and Functional Analysis of Validoxylamine A 7′-phosphate Synthase ValL Involved in Validamycin A Biosynthesis

Validamycin A (Val-A) is an effective antifungal agent widely used in Asian countries as crop protectant. Validoxylamine A, the core structure and intermediate of Val-A, consists of two C7-cyclitol units connected by a rare C-N bond. In the Val-A biosynthetic gene cluster in Streptomyces hygroscopicus 5008, the ORF valL was initially annotated as a validoxylamine A 7′-phosphate(V7P) synthase, whose encoded 497-aa protein shows high similarity with trehalose 6-phosphate(T6P) synthase. Gene inactivation of valL abolished both validoxylamine A and validamycin A productivity, and complementation with a cloned valL recovered 10% production of the wild-type in the mutant, indicating the involvement of ValL in validoxylamine A biosynthesis. Also we determined the structures of ValL and ValL/trehalose complex. The structural data indicates that ValL adopts the typical fold of GT-B protein family, featuring two Rossmann-fold domains and an active site at domain junction. The residues in the active site are arranged in a manner homologous to that of Escherichia coli (E.coli) T6P synthase OtsA. However, a significant discrepancy is found in the active-site loop region. Also noticeable structural variance is found around the active site entrance in the apo ValL structure while the region takes an ordered configuration upon binding of product analog trehalose. Furthermore, the modeling of V7P in the active site of ValL suggests that ValL might have a similar SNi-like mechanism as OtsA

Minimum Information about a Biosynthetic Gene cluster

A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.Chemistry and Chemical Biolog

Considerations for hypothetical carbon dioxide removal via alkalinity addition in the Amazon River watershed

The Amazon River plume plays a critical role in shaping the carbonate chemistry over a vast area in the western tropical North Atlantic. We conduct a sensitivity analysis of hypothetical ocean alkalinity enhancement (OAE) via quicklime addition in the Amazon River watershed, examining the response of carbonate chemistry and air-sea carbon dioxide flux to the alkalinity addition. Through a series of sensitivity tests, we show that the detectability of the OAE-induced alkalinity increment depends on the perturbation strength (or size of the alkalinity addition, I TA) and the number of samples: there is a 90 % chance to meet a minimum detectability requirement with I TA 15 μmolkg-1 and sample size \u3e40, given background variability of 15-30 μmolkg-1. OAE-induced pCO2 reduction at the Amazon plume surface would range between 0-25 μatm when I TACombining double low line20 μmolkg-1, decreasing with increasing salinity (S). Adding 20 μmolkg-1 of alkalinity at the river mouth could elevate the total carbon uptake in the Amazon River plume (1532) due to its large size, comprising approximately 80 % of the S\u3e15 plume area. However, the lowest-salinity region (S\u3c15) has a greater drop in surface ocean partial pressure of CO2 (pCO2sw) due to its low buffer capacity, potentially allowing for observational detectability of pCO2sw reduction in this region. Reduced outgassing in this part of the plume, while more uncertain, may also be important for total additional CO2 uptake. Such sensitivity tests are useful in designing minimalistic field trials and setting achievable goals for monitoring, reporting, and verification purposes