YHP: Y-chromosome Haplogroup Predictor for predicting male lineages based on Y-STRs

Abstract

Human Y chromosome reflects the evolutionary process of males. Male lineage tracing by Y chromosome is of great use in evolutionary, forensic, and anthropological studies when male samples exist or especially when the biological sample is a mixture of male and female individuals. Identifying the male lineage based on the specific distribution of Y haplogroups narrows down the investigation scope. Integrating previously published datasets with genotypes of Y chromosome short tandem repeats (Y-STRs) and high-resolution haplogroups (122 haplogroups in total), we developed YHP (Y Haplogroup Predictor), an open-access and userfriendly software package to predict haplogroups, compare the similarity, and conduct mismatch analysis of samples with Y-STR profiles. The software is available at Github (https://github.com/cissy123/YHP-Y-Haplogroup-Predictor-).Author SummaryFamilial searching has been used in forensic, anthropologic, and personalized scenarios. Software packages have been developed to assist in male familial searching, such as predicting Y-SNP haplogroups by Y-STRs. However, these software packages, in general, achieve this goal with a rough resolution. In this study, we developed a software package to conduct high-resolution haplogroup inference to help familial searching and at the same time reduce the cost, since it does not require tiresome Y-SNP sequencing.

Multivalent Polymer–Peptide Conjugates: A General Platform for Inhibiting Amyloid Beta Peptide Aggregation

“…With the same polymer backbone, mPPCs with 7% LD loading were better inhibitors than those with 3% or 12% loading. 10 We further reported that mPPCs at a constant 7% LD loading disassemble mature fibrils with a dependence on polymer MW. 11,12 However, it remains unclear 1) if the conjugation strategy is applicable to ligands other LD; 2) how the ligand loading and polymer MW affect mPPC inhibition potency in tandem; and 3) what the origin of such dependence is at the molecular level.…”

“…10 We further reported that mPPCs at a constant 7% LD loading disassemble mature fibrils with a dependence on polymer MW. 11,12 However, it remains unclear 1) if the conjugation strategy is applicable to ligands other LD; 2) how the ligand loading and polymer MW affect mPPC inhibition potency in tandem; and 3) what the origin of such dependence is at the molecular level. Here we report the preparation and inhibition properties of mPPCs of three different ligands, with systematic investigation of ligand loading and polymer MW.…”

“…The MWs and loading percentages were chosen based on previous results. 10,11,19 We aimed to prepare LD-and LN-mPPCs of 3-12% loading to test whether 7% loading is optimal for LD-mPPCs of all MWs 10 and how such dependence varies for mPPCs bearing a neutral ligand LN. A higher ligand loading (7-15%) for GA-mPPCs was targeted since GA was reported to be ineffective without a strongly hydrogen-bonding thymine moiety at the N-terminus.…”

The Chemistry and Biology of Bactobolin: A 10-Year Collaboration with Natural Product Chemist Extraordinaire Jon Clardy

“…Several studies implicated QS-1 and, to a lesser extent, QS-3 of B. pseudomallei in animal infections. [11][12][13] The QS systems of B. mallei were also initially shown to contribute to virulence. 14 Although later results did not corroborate these initial findings, 15 the conservation of QS-1 and QS-3 in B. mallei supported the idea that these two systems play a role during survival in the host.…”

“…HR-MS analysis of the most abundant bactobolin variant, bactobolin A, was consistent with the presence of two chlorine substituents. Indeed, a singlet deshielded peak at 6.18 ppm, with a corresponding 74 ppm 13 C shift, was symptomatic of a methine-carbon carrying two chlorine substituents. The structure of bactobolin A was ultimately solved by analysis of a full suite of 1D/2D NMR spectra and shown to be identical to that previously solved by Kondo and co-workers (Figure 1b).…”