Effects of Phenyllactic Acid, Lactic Acid Bacteria, and Their Mixture on Fermentation Characteristics and Microbial Community Composition of Timothy Silage

This study investigated the effects of phenyllactic acid (PL), lactic acid bacteria (LAB), and their mixture on fermentation characteristics and microbial community composition of timothy silage. Timothy silages were treated without (CK) or with PL [10 mg/kg fresh matter (FM) basis], LAB inoculant (IN; a mixture of Lactobacillus plantarum and L.buchneri, 105 cfu/g FM), and their mixture (PI) and stored at ambient temperature (5°C∼15°C) in a dark room for 60 days. Compared with CK, all treated silages showed lower (P < 0.05) levels of butyric acid and ammonia-N. Treatment with PL enhanced (P < 0.05) the crude protein preservation of silage by favoring the growth of L. curvatus and Saccharomyces cerevisiae and inhibition of lactic acid–assimilating yeast belonging to Issatchenkia during ensiling. In particular, treatment with PL advanced (P < 0.05) the productions of lactic acid and volatile fatty acid in IN-treated silage. Therefore, PL used as a new additive exhibited potential for improving silage fermentation when it is combined with LAB IN during ensiling.

Taphonomic and Diagenetic Pathways to Protein Preservation, Part I: The Case of Tyrannosaurus rex Specimen MOR 1125

Many recent reports have demonstrated remarkable preservation of proteins in fossil bones dating back to the Permian. However, preservation mechanisms that foster the long-term stability of biomolecules and the taphonomic circumstances facilitating them remain largely unexplored. To address this, we examined the taphonomic and geochemical history of Tyrannosaurus rex specimen Museum of the Rockies (MOR) 1125, whose right femur and tibiae were previously shown to retain still-soft tissues and endogenous proteins. By combining taphonomic insights with trace element compositional data, we reconstruct the postmortem history of this famous specimen. Our data show that following prolonged, subaqueous decay in an estuarine channel, MOR 1125 was buried in a coarse sandstone wherein its bones fossilized while interacting with oxic and potentially brackish early-diagenetic groundwaters. Once its bones became stable fossils, they experienced minimal further chemical alteration. Comparisons with other recent studies reveal that oxidizing early-diagenetic microenvironments and diagenetic circumstances which restrict exposure to percolating pore fluids elevate biomolecular preservation potential by promoting molecular condensation reactions and hindering chemical alteration, respectively. Avoiding protracted interactions with late-diagenetic pore fluids is also likely crucial. Similar studies must be conducted on fossil bones preserved under diverse paleoenvironmental and diagenetic contexts to fully elucidate molecular preservation pathways.

Palaeoproteomic analyses of dog palaeofaeces reveal a preserved dietary and host digestive proteome

The domestic dog has inhabited the anthropogenic niche for at least 15 000 years, but despite their impact on human strategies, the lives of dogs and their interactions with humans have only recently become a subject of interest to archaeologists. In the Arctic, dogs rely exclusively on humans for food during the winter, and while stable isotope analyses have revealed dietary similarities at some sites, deciphering the details of provisioning strategies have been challenging. In this study, we apply zooarchaeology by mass spectrometry (ZooMS) and liquid chromatography tandem mass spectrometry to dog palaeofaeces to investigate protein preservation in this highly degradable material and obtain information about the diet of domestic dogs at the Nunalleq site, Alaska. We identify a suite of digestive and metabolic proteins from the host species, demonstrating the utility of this material as a novel and viable substrate for the recovery of gastrointestinal proteomes. The recovered proteins revealed that the Nunalleq dogs consumed a range of Pacific salmon species (coho, chum, chinook and sockeye) and that the consumed tissues derived from muscle and bone tissues as well as roe and guts. Overall, the study demonstrated the viability of permafrost-preserved palaeofaeces as a unique source of host and dietary proteomes.

Evaluation of RNAlater™ as a field-compatible preservation method for metaproteomic analyses of bacteria-animal symbioses

Field studies are central to environmental microbiology and microbial ecology as they enable studies of natural microbial communities. Metaproteomics, the study of protein abundances in microbial communities, allows to study these communities ‘in situ’ which requires protein preservation directly in the field as protein abundance patterns can change rapidly after sampling. Ideally, a protein preservative for field deployment works rapidly and preserves the whole proteome, is stable in long-term storage, is non-hazardous and easy to transport, and is available at low cost. Although these requirements might be met by several protein preservatives, an assessment of their suitability in field conditions when targeted for metaproteomics is currently lacking. Here, we compared the protein preservation performance of flash freezing and the preservation solution RNAlater™ using the marine gutless oligochaete Olavius algarvensis and its symbiotic microbes as a test case. In addition, we evaluated long-term RNAlater™ storage after 1 day, 1 week and 4 weeks at room temperature (22-23 °C). We evaluated protein preservation using one dimensional liquid chromatography tandem mass spectrometry (1D-LC-MS/MS). We found that RNAlater™ and flash freezing preserved proteins equally well in terms of total number of identified proteins or relative abundances of individual proteins and none of the test time points were altered compared to t0. Moreover, we did not find biases against specific taxonomic groups or proteins with particular biochemical properties. Based on our metaproteomics data and the logistical requirements for field deployment we recommend RNAlater™ for protein preservation of field-collected samples when targeted for metaproteomcis.

Reduced ATP-dependent proteolysis of functional proteins during nutrient limitation speeds the return of microbes to a growth state

When cells run out of nutrients, the growth rate greatly decreases. Here, we report that microorganisms, such as the bacterium Salmonella enterica serovar Typhimurium, speed up the return to a rapid growth state by preventing the proteolysis of functional proteins by ATP-dependent proteases while in the slow-growth state or stationary phase. This reduction in functional protein degradation resulted from a decrease in the intracellular concentration of ATP that was nonetheless sufficient to allow the continued degradation of nonfunctional proteins by the same proteases. Protein preservation occurred under limiting magnesium, carbon, or nitrogen conditions, indicating that this response was not specific to low availability of a particular nutrient. Nevertheless, the return to rapid growth required proteins that mediate responses to the specific nutrient limitation conditions, because the transcriptional regulator PhoP was necessary for rapid recovery only after magnesium starvation. Reductions in intracellular ATP and in ATP-dependent proteolysis also enabled the yeast Saccharomyces cerevisiae to recover faster from stationary phase. Our findings suggest that protein preservation during a slow-growth state is a conserved microbial strategy that facilitates the return to a growth state once nutrients become available.

Mechanisms of soft tissue and protein preservation in Tyrannosaurus rex

The idea that original soft tissue structures and the native structural proteins comprising them can persist across geological time is controversial, in part because rigorous and testable mechanisms that can occur under natural conditions, resulting in such preservation, have not been well defined. Here, we evaluate two non-enzymatic structural protein crosslinking mechanisms, Fenton chemistry and glycation, for their possible contribution to the preservation of blood vessel structures recovered from the cortical bone of a Tyrannosaurus rex (USNM 555000 [formerly, MOR 555]). We demonstrate the endogeneity of the fossil vessel tissues, as well as the presence of type I collagen in the outermost vessel layers, using imaging, diffraction, spectroscopy, and immunohistochemistry. Then, we use data derived from synchrotron FTIR studies of the T. rex vessels to analyse their crosslink character, with comparison against two non-enzymatic Fenton chemistry- and glycation-treated extant chicken samples. We also provide supporting X-ray microprobe analyses of the chemical state of these fossil tissues to support our conclusion that non-enzymatic crosslinking pathways likely contributed to stabilizing, and thus preserving, these T. rex vessels. Finally, we propose that these stabilizing crosslinks could play a crucial role in the preservation of other microvascular tissues in skeletal elements from the Mesozoic.

Comparison of Fixation Methods for Preservation Cytology Specimens of Cell Block Preparation Using 10% Neutral Buffer Formalin and 96% Alcohol Fixation in E-cadherin and Ki-67 Immunohistochemical Examination

BACKGROUND: Cytological and molecular examinations are among the most important examinations in cancer diagnosis. 96% alcohol is a fixative solution commonly used by clinicians for cytological samples because of its accessibility and affordability. Cellblock preparation from cytology specimen may increase morphology detail and may be used for further biomarker analysis. E-cadherin is an adhesion protein expressed in the cell membrane of most carcinoma. Ki67 is a protein expressed in nuclei of malignant cells that used as a proliferation marker. AIM: This study was designed to investigate the effect of fixation duration in 96% alcohol on protein preservation for immunohistochemistry (IHC) evaluation compared to 10% neutral buffered formalin (NBF) as the gold standard. METHODS: Twenty-five fine-needle aspiration biopsy (FNAB) specimen diagnosed as carcinoma were fixed in 10% NBF and 96% alcohol for 1 hour, 6 hours, 24 hours, 48 hours and 72 hours. Cell blocks preparation were made from those 6 groups of specimens. E-cadherin and Ki67 IHC were done to cell blocks section and evaluated. The data were statistically analysed using the Friedman test with p-value < 0.05 of a significant level. RESULTS: There were significant differences between E-cadherin and Ki67 expression in cell block preparation from 96% alcohol-fixed cytology specimen for 1 hour, 6 hours, 24 hours, 48 hours and 72 hours to 10% NBF (p = 0.0001). CONCLUSION: The result indicated that 96% alcohol is not suitable as a fixative solution for cell block preparation in E-cadherin and Ki-67 IHC examination.