Biology subjects

Peretti, A.

Publications and source records attributed to Peretti, A..

5 recordsLinked to original sources

bioRxiv2022

A Multivalent Polyomavirus Vaccine Elicits Durable Neutralizing Antibody Responses in Macaques

In 2019, there were about 100,000 kidney transplants globally, with more than a quarter of them performed in the United States. Unfortunately, some engrafted organs are lost to polyomavirus-associated nephropathy (PyVAN) caused by BK and JC viruses (BKPyV and JCPyV). Transplant patients are routinely monitored for BKPyV viremia, which is an accepted hallmark of nascent nephropathy. If viremia is detected, a reduction in immunosuppressive therapy is standard care, but the intervention comes with increased risk of immune rejection of the engrafted organ. Recent reports have suggested that transplant recipients with high levels of polyomavirus-neutralizing antibodies are protected against PyVAN. Virus-like particle (VLP) vaccines, similar to approved human papillomaviruses vaccines, have an excellent safety record and are known to induce high levels of neutralizing antibodies associated and long-lasting protection from infection. In this study, we demonstrate that VLPs representing BKPyV genotypes I, II, and IV, as well as JCPyV genotype 2 produced in insect cells elicit robust antibody titers. In rhesus macaques, all monkeys developed neutralizing antibody titers above a previously proposed protective threshold of 10,000. A second inoculation, administered 19 weeks after priming, boosted titers to a plateau of [≥]25,000 that was maintained for almost two years. No vaccine-related adverse events were observed in any macaques. A multivalent BK/JC VLP immunogen did not show inferiority compared to the single-genotype VLP immunogens. Considering these encouraging results, we believe a clinical trial administering the multivalent VLP vaccine in patients waiting to receive a kidney transplant is warranted to evaluate its ability to reduce or eliminate PyVAN. HIGHLIGHTSO_LIRecombinant virus-like particle vaccine was safely administered to rhesus macaques C_LIO_LIVaccination generated high-titer neutralizing antibody responses C_LIO_LIMultivalent BK/JC polyomavirus vaccine was as effective as monovalent vaccines C_LIO_LIHigh neutralizing titers were sustained for 92 weeks without appreciable decline C_LI

immunology↗

bioRxiv2020

Three-dimensionally preserved 'Stage IIIb' fossil down feather supports developmental modularity in feather evolution

We describe a unique three-dimensionally preserved fossil down feather from the Late Cretaceous of Myanmar. Its morphology is highly congruent with Stage IIIb of the widely accepted Prum and Brush model of feather evolution-development. This makes the new specimen the first evidence of this developmental stage in the fossil record. The Stage IIIb diagnosis is robustly supported by the absence of a central rachis and by its paired barbules emanating from radially positioned barbs that are attached to a short calamus. Prum and Brushs model hypothesises a bifurcation in the evolution-development pathway at Stage III. Stage IIIa involves rachis development and branching into barbs. Stage IIIb involves branching of the barbs from the calamus and then further branching of the barbules from the barbs. These two pathways then converge into Stage IIIa+b where feathers produce a rachis, barbs and barbules in nested order, finally leading to Stage IV. Evolution-development studies on the morphogenesis of feathers have unequivocally shown that such feather branching can be controlled by BMP, Noggin, Shh and several other proteins. Therefore, molecular crosstalk can convert a barb into a rachis and vice versa. The topology of this down feather, consistent with specific patterns of modular protein-protein signalling already observed, provides the first definitive evidence that such signalling was responsible for the evolution of a diverse inventory of feather morphologies in non-avialan dinosaurs and early birds since the middle Jurassic.

paleontology↗

bioRxiv2020

The tiny Cretaceous stem-bird Oculudentavis revealed as a bizarre lizard

Oculudentavis khaungraae was described based on a tiny skull trapped in amber. The slender tapering rostrum with retracted osseous nares, large eyes, and short vaulted braincase led to its identification as the smallest avian dinosaur on record, comparable to the smallest living hummingbirds. Despite its bird-like appearance, Oculudentavis showed several features inconsistent with its original phylogenetic placement. Here we describe a more complete, specimen that demonstrates Oculudentavis is actually a bizarre lizard of uncertain position. The new interpretation and phylogenetic placement highlights a rare case of convergent evolution rarely seen among reptiles. Our results re-affirm the importance of Myanmar amber in yielding unusual taxa from a forest ecosystem rarely represented in the fossil record.

paleontology↗

bioRxiv2020

One-shot analysis of translated mammalian lncRNAs with AHARIBO

A vast portion of the mammalian genome is transcribed as long non-coding RNAs (lncRNAs) acting in the cytoplasm with largely unknown functions. Surprisingly, lncRNAs have been shown to interact with ribosomes, encode uncharacterized proteins, or act as ribosome sponges. These functions still remain mostly undetected and understudied owing to the lack of efficient tools for genome-wide simultaneous identification of ribosome-associated lncRNAs and peptide-producing lncRNAs. Here we present AHARIBO, a method for the detection of lncRNAs either untranslated, but associated with ribosomes, or encoding small peptides. Using AHARIBO in mouse embryonic stem cells during neuronal differentiation, we isolated ribosome-protected RNA fragments, translated RNAs and corresponding de novo synthesized polypeptides. Besides identifying mRNAs under active translation and associated ribosomes, we found and distinguished lncRNAs acting as ribosome sponges or encoding micropeptides, laying the ground for a better functional understanding of hundreds lncRNAs.

cell biology↗

bioRxiv2019

Discovery of several thousand highly diverse circular DNA viruses

Although it is suspected that there are millions of distinct viral species, fewer than 9,000 are catalogued in GenBanks RefSeq database. We selectively enriched for and amplified the genomes of circular DNA viruses in over 70 animal samples, ranging from cultured soil nematodes to human tissue specimens. A bioinformatics pipeline, Cenote-Taker, was developed to automatically annotate over 2,500 circular genomes in a GenBank-compliant format. The new genomes belong to dozens of established and emerging viral families. Some appear to be the result of previously undescribed recombination events between ssDNA viruses and ssRNA viruses. In addition, hundreds of circular DNA elements that do not encode any discernable similarities to previously characterized sequences were identified. To characterize these "dark matter" sequences, we used an artificial neural network to identify candidate viral capsid proteins, several of which formed virus-like particles when expressed in culture. These data further the understanding of viral sequence diversity and allow for high throughput documentation of the virosphere.

microbiology↗