“What is history but a fable agreed upon.” So wrote Napoleon Bonaparte, a man considered by many to be a tactical genius and by others to be a bloody butcher. Reality lies somewhere between, part of the fable. Defined as “a narrative making a cautionary point . . . a story about legendary persons or exploits . . . [or] a falsehood,” the term fable characterizes, in a positive and a negative sense, the treatment of many historic episodes, including the Navajo Long Walk period. Much has been written of this time when the Navajo people, following what appears to be a fairly short resistance, surrendered in droves to the US military, collected at Fort Defiance and other designated sites, then moved in a series of “long walks” to Fort Sumner (Hwéeldi) on the Pecos River in eastern New Mexico. There was much that preceded these events. Stretching back to the beginning of Euro-American occupation of the Southwest, the Spanish initiated a slave trade against the “wild” or unsettled (non-Puebloan) Indians that pitted various groups against their neighbors. Two major players in the arena were the Utes and Navajos. They shared relatively few years of peace, remaining gener- ally in a state of warfare that simmered somewhere between hostility and open conflict. As with so many colonial wars, the beginning of these tit-for-tat reprisals is lost to history, but its constancy is not. Spanning the Spanish, Mexican, and early territorial period of the American Southwest, the slave trade was a prime source of fuel for intertribal conflict and provided the owner of captive Indians with labor to enhance comfort and spur economic development. Much of what characterized this period of history and Navajo/Ute relations is comparable to what happened to other peoples in different settings.

Antibody phage display libraries combined with high-throughput selections have recently demonstrated tremendous promise to create the next generation of renewable, recombinant antibodies to study proteins and their many post-translational modification states; however, many challenges still remain, such as optimized antibody scaffolds. Recently, a single-chain fragment antigen binding (Fab) (scFab) format, in which the carboxy-terminus of the light chain is linked to the amino-terminus of the heavy chain, was described to potentially combine the high display levels of a single-chain fragment variable with the high stability of purified Fabs. However, this format required removal of the interchain disulfide bond to achieve modest display levels and subsequent bacterial expression resulted in high levels of aggregated scFab, hindering further use of scFabs. Here, we developed an improved scFab format that retains the interchain disulfide bond by increasing the linker length between the light and heavy chains to improve display and bacterial expression levels to 1-3 mg/L. Furthermore, rerouting of the scFab to the co-translational signal recognition particle pathway combined with reengineering of the signal peptide sequence results in display levels 24-fold above the original scFab format and 3-fold above parent Fab levels. This optimized scFab scaffold can be easily reformatted in a single step for expression in a bacterial or mammalian host to produce stable (Tm of 81 °C), predominantly monomeric (>90%) antibodies at a high yield. Ultimately, this new scFab format will advance high-throughput antibody generation platforms to discover the next generation of research and therapeutic antibodies.

Differential scanning fluorimetry (DSF) is a widely used technique for determining the apparent melting temperature (Tma) of a purified protein. Here, we present a protocol for performing and optimizing DSF experiments. We describe steps for designing and performing the experiment, analyzing data, and optimization. We provide benchmarks for typical Tmas and ΔTmas, standard assay conditions, and upper and lower limits of commonly altered experimental variables. We also detail common pitfalls of DSF and ways to avoid, identify, and overcome them.

Bovine digital dermatitis (BDD) is a multifactorial polymicrobial infectious disease associated with multiple species and phylotypes of treponemes. However, despite the abundance of molecular signatures for treponemes that are identified in bovine lesions, relatively few isolates are cultured, and even fewer have been characterized at the level of protein expression. Here we report the successful isolation and characterization of novel strains of T. brennaborense and T. phagedenis from cases of BDD in Iowa dairy cows, and compare them to a well characterized strain of T. phagedenis, and the type strain of the more recently recognized T. pedis. Propagation of T. brennaborense was only possible at room temperature in Cooked Meat Medium, and not in oral treponeme enrichment medium at 37 °C as used for T. phagedenis and T. pedis. A prominent and rapid motility is observed by T. brennaborense under dark-field microscopy. The highly motile T. brennaborense strain 11-3 has an identical enzymatic profile to that of the only other isolate of T. brennaborense to be cultured from a lesion of BDD. Outer membrane protein profiles of each strain were compared by 2-D gel electrophoresis, and the five most abundant proteins in each strain were identified by mass spectrometry. All identified proteins are predicted to have signal peptides. Results identified outer membrane proteins specific to each strain including predicted membrane lipoproteins, ABC transporters and, as yet, uncharacterized proteins. Collectively, our results provide for the identification and characterization of outer membrane components of multiple phylotypes of treponemes associated with BDD which can facilitate development of vaccines and diagnostics in our efforts to eradicate the disease.

This illustrated brochure provides a report on the National Center for Geographic Information and its activities in the period 1 December 1988 through 30 December 1994. It features the Center's primary research initiatives; its role as a clearinghouse for disseminating information in support of GIS research, teaching, and applications; and its activities in education on behalf of curriculum development and support for teachers and professional training. Separate sections describe the personnel associated with the project, the unique research associated with each of  the three institutional partners (UC Santa Barbara, SUNY at Buffalo, and the University of Maine) and the collaborative activities that link these partners for the fulfillment of common objectives.

Heterochromatin protein 1 (HP1) family proteins are conserved chromatin binding proteins involved in gene silencing, chromosome packaging, and chromosome segregation. These proteins recognize histone H3 lysine 9 methylated tails via their chromodomain and recruit additional ligand proteins with diverse activities through their dimerization domain, the chromoshadow domain. Species that have HP1 proteins possess multiple paralogs that perform non-overlapping roles in vivo. How different HP1 proteins, which are highly conserved, perform different functions is not well understood. Here, we use the two Schizosaccharomyces pombe HP1 paralogs, Swi6 and Chp2, as model systems to compare and contrast their biophysical properties. We find that Swi6 and Chp2 have similar dimerization and oligomerization equilibria, and that Swi6 binds slightly (~3-fold) more strongly to nucleosomes than Chp2. Furthermore, while Swi6 binding to the H3K9me3 mark is regulated by a previously described auto-inhibition mechanism, the binding of Chp2 to the H3K9me3 mark is not analogously regulated. In the context of chromoshadow domain interactions, we show using a newly identified peptide sequence from the Clr3 histone deacetylase and a previously identified sequence from the protein Shugoshin that the Swi6 chromoshadow domain binds both ligands more strongly than the Chp2. Overall, our findings uncover quantitative differences in how Swi6 and Chp2 interact with nucleosomal and non-nucleosomal ligands and qualitative differences in how their assembly on nucleosomes is regulated. These findings provide a biochemical framework to explain the varied functions of Chp2 and Swi6 in vivo.

Digital Frequency-Domain Multiplexing (DfMux) is a technique that uses MHz superconducting resonators and Superconducting Quantum Interference Device (SQUID) arrays to read out sets of transition edge sensors. DfMux has been used by several Cosmic Microwave Background experiments, including most recently POLARBEAR-2 and SPT-3 G with multiplexing factors as high as 68, and is the baseline readout technology for the planned satellite mission LiteBIRD. Here, we present recent work focused on improving DfMux readout noise, reducing parasitic impedance, and improving sensor operation. We have achieved a substantial reduction in stray impedance by integrating the sensors, resonators, and SQUID array onto a single-carrier board operated at 250 mK. This also drastically simplifies the packaging of the cryogenic components and leads to better-controlled crosstalk. We demonstrate a low readout noise level of 8.6 pA / Hz 1 1 / 2, which was made possible by operating the SQUID array at a reduced temperature and with a low dynamic impedance. This is a factor of two improvement compared to the achieved readout noise level in currently operating Cosmic Microwave Background experiments using DfMux and represents a critical step toward maturation of the technology for the next generation of instruments.

Cysteine can be specifically functionalized by a myriad of acid-base conjugation strategies for applications ranging from probing protein function to antibody-drug conjugates and proteomics. In contrast, selective ligation to the other sulfur-containing amino acid, methionine, has been precluded by its intrinsically weaker nucleophilicity. Here, we report a strategy for chemoselective methionine bioconjugation through redox reactivity, using oxaziridine-based reagents to achieve highly selective, rapid, and robust methionine labeling under a range of biocompatible reaction conditions. We highlight the broad utility of this conjugation method to enable precise addition of payloads to proteins, synthesis of antibody-drug conjugates, and identification of hyperreactive methionine residues in whole proteomes.