High resolution maps of chromatin reorganization through mouse meiosis reveal novel features of the 3D meiotic structure.

When germ cells transition from the mitotic cycle into meiotic prophase I (MPI), chromosomes condense into an array of chromatin loops that are required to promote homolog pairing and genetic recombination. To identify the changes in chromosomal conformation, we isolated nuclei on a trajectory from spermatogonia to the end of MPI. At each stage along this trajectory, we built genomic interaction maps with the highest temporal and spatial resolution to date. The changes in chromatin folding coincided with a concurrent decline in mitotic cohesion and a rise in meiotic cohesin complexes. We found that the stereotypical large-scale A and B compartmentalization was lost during meiotic prophase I alongside the loss of topological associating domains (TADs). Still, local subcompartments were detected and maintained throughout meiosis. The enhanced Micro-C resolution revealed that, despite the loss of TADs, higher frequency contact sites between two loci were detectable during meiotic prophase I coinciding with CTCF bound sites. The pattern of interactions around these CTCF sites with their neighboring loci showed that CTCF sites were often anchoring the meiotic loops. Additionally, the localization of CTCF to the meiotic axes indicated that these anchors were at the base of loops. Strikingly, even in the face of the dramatic reconfiguration of interphase chromatin into a condensed loop-array, the interactions between regulatory elements remained well preserved. This establishes a potential mechanism for how the meiotic chromatin maintains active transcription within a highly structured genome. In summary, the high temporal and spatial resolution of these data revealed previously unappreciated aspects of mammalian meiotic chromatin organization.

Cataloging Human PRDM9 Allelic Variation Using Long-Read Sequencing Reveals PRDM9 Population Specificity and Two Distinct Groupings of Related Alleles.

The PRDM9 protein determines sites of meiotic recombination in humans by directing meiotic DNA double-strand breaks to specific loci. Targeting specificity is encoded by a long array of C2H2 zinc fingers that bind to DNA. This zinc finger array is hypervariable, and the resulting alleles each have a potentially different DNA binding preference. The assessment of PRDM9 diversity is important for understanding the complexity of human population genetics, inheritance linkage patterns, and predisposition to genetic disease. Due to the repetitive nature of the PRDM9 zinc finger array, the large-scale sequencing of human PRDM9 is challenging. We, therefore, developed a long-read sequencing strategy to infer the diploid PRDM9 zinc finger array genotype in a high-throughput manner. From an unbiased study of PRDM9 allelic diversity in 720 individuals from seven human populations, we detected 69 PRDM9 alleles. Several alleles differ in frequency among human populations, and 32 alleles had not been identified by previous studies, which were heavily biased to European populations. PRDM9 alleles are distinguished by their DNA binding site preferences and fall into two major categories related to the most common PRDM9-A and PRDM9-C alleles. We also found that it is likely that inter-conversion between allele types is rare. By mapping meiotic double-strand breaks (DSBs) in the testis, we found that small variations in PRDM9 can substantially alter the meiotic recombination landscape, demonstrating that minor PRDM9 variants may play an under-appreciated role in shaping patterns of human recombination. In summary, our data greatly expands knowledge of PRDM9 diversity in humans.

Comparative gene expression analysis in mouse models for identifying critical pathways in mammary gland development.

Functional development of the mammary gland is an important physiological process. Several studies have used gene expression profiling of mammary gland development to identify the key genes in the process, but few focused on the involved pathways. And there is a lack of concordance between those observed pathways. In this article, we applied a standardized microarray preprocessing to four independent studies, and then used gene set enrichment analysis (GSEA) to identify the key pathways. The result demonstrated an increased concordance between these expression profiling data sets. From the stage of puberty to pregnancy, we found 7 up-regulated and 6 down-regulated pathways in common. From the period of pregnancy to lactation, we found 7 up-regulated and 58 down-regulated pathways in common. And 10 up-regulated and 3 down-regulated pathways were found in common from lactation to the involution period. The main canonical pathways identified belong to immune system, cell communication, metabolism, and disease-related pathways. Pathway analysis is a more effective method than single gene analysis because the former one can able to detect genes weakly connected to the phenotype. As we applied GSEA to the study, our findings suggested a greater concordance in this physiological process. The critical pathways we find can provide some insight of functional development of the mammary gland and motivate other relative studies.

Antioxidant, antihypertensive, and immunomodulatory activities of peptide fractions from fermented skim milk with Lactobacillus delbrueckii ssp. bulgaricus LB340.

The aim of this study was to evaluate the antioxidant, antihypertensive and immunomodulatory characteristics of skim milk fermented with Lactobacillus delbrueckii ssp. bulgaricus LB340. Supernatants obtained from the ferments after centrifugation were subjected to ultrafiltration and yielded four peptidic fractions of 10-5 kDa, 5-3 kDa, 3-1 kDa, and <1·0 kDa. Peptides in 5-3 kDa range exhibited a good antioxidant activity. The peptides (<1·0 k) was applied to Superdex-30 G column fractionation and produced six fractions (F1-6). Fraction F2 presented the highest angiotensin I-converting enzyme inhibition activity with IC50 of 67·71 ± 7·62 mg/ml. Moreover, fraction F6, which displayed a good immunomodulatory activity, had a positive effect on murine spleen lymphocyte proliferation with Stimulation Index of 0·729 ± 0·123. The present data showed the potential of the milk fermented with Lactobacillus delbrueckii ssp. bulgaricus LB340 as a functional food, however, further research is needed to evaluate the biofunctional activity of this fermentation product in vivo using model animal.

[Spectrum recovery method for interferometric data].

The interferometric data acquired by Fourier transform spectrometer was a betweenness which couldn't be used directly. For the successful application of the interferometric data, spectrum recovery processing must be adopted. The conventional method based on inverse Fourier transform was frequently used for spectrum recovery. According to the principle analysis of the interferometric data, the mixing model was induced, and the spectrum recovery method based on the mixing model of the interferometric data was presented. Finally, the computer simulation for these two methods mentioned above was implemented, and the recovered spectra were compared with the standard spectrum. The simulation results indicated that the spectral precision of the new method was better than the conventional method, which provided a new scheme for spectrum recovery.