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The human genome is composed of distinct genomic regions that are susceptible to various types of somatic mutations. Among these, Short Tandem Repeats (STRs) stand out as the most mutable genetic elements. STRs are short repetitive polymorphic sequences, predominantly situated within noncoding sectors of the genome. The intrinsic repetition characterizing these sequences makes them highly mutable in vivo. Consequently, this characteristic provides the chance to unravel the natural developmental history of human viable cells retrospectively. However, STRs also introduce stutter noise in vitro amplification, which makes their analysis challenging. Here we describe our integrated biochemical-computational platform for single-cell lineage analysis. It consists of a pipeline whose inputs are single cells and whose output is a lineage tree of input cells., (© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Objective: Biased interoception decoupled from physiology might be relevant in the etiology of pathological illness anxiety (PIA). Empirical evidence for interoceptive deviations in illness anxiety is scarce but potentially informative to optimize treatments. We hypothesized that persons with PIA differ fundamentally in the classification of bodily sensations from those without PIA., Methods: In a respiratory categorization task, participants breathed into a pulmonary training device. Inspiration effort was varied by eight resistive loads. The lower/higher four loads were introduced as belonging to arbitrary categories "A"/"B," respectively. Participants memorized respiratory sensations in a first experimental block and were asked to label the resistances in a second block. We calculated the sensitivity of resistance classification according to category and response bias in terms of categorical misclassification. Data of 39 participants with PIA and 35 controls were compared with regard to sensitivity and response bias by group, resistive load, and their interaction in a multiple regression., Results: With similar sensitivity, patients more often labeled loads above the categorical border erroneously as belonging to category A, thus underestimating their resistance ( β = -0.06, p = .001; η2 = 0.02)., Conclusions: Individuals with PIA showed a systematic "wait and see" approach. Altered respiroception in PIA might stem from biased perception during training phase, the recognition phase, biased memory, or a combination of these. Its exact characteristics remain unknown, and future research must address the challenge of developing reliable and valid paradigms accounting for the variability of interoceptive biases., Registration: This work was preregistered on OSF ( https://osf.io/9shcw )., (Copyright © 2023 by the American Psychosomatic Society.)

Short tandem repeats (STRs) are highly abundant in the human genome, but existing approaches for accurate genotyping of STRs are limited. Here, we describe a protocol for duplex molecular inversion probes for high-throughput and cost-effective STR enrichment. We have successfully tested panels targeting as many as 50K STRs in several thousands of genomic samples (e.g., HeLa cells, Du145 cells, leukemia cells, melanoma cells). However, because the protocol is plate based, the sample size is limited to a few thousand. For complete details on the use and execution of this protocol, please refer to Tao et al. (2021)., Competing Interests: The authors declare no competing interests., (© 2021 The Authors.)

Cell lineage analysis aims to uncover the developmental history of an organism back to its cell of origin. Recently, novel in vivo methods utilizing genome editing enabled important insights into the cell lineages of animals. In contrast, human cell lineage remains restricted to retrospective approaches, which still lack resolution and cost-efficient solutions. Here, we demonstrate a scalable platform based on short tandem repeats targeted by duplex molecular inversion probes. With this human cell lineage tracing method, we accurately reproduced a known lineage of DU145 cells and reconstructed lineages of healthy and metastatic single cells from a melanoma patient who matched the anatomical reference while adding further refinements. This platform allowed us to faithfully recapitulate lineages of developmental tissue formation in healthy cells. In summary, our lineage discovery platform can profile informative somatic mutations efficiently and provides solid lineage reconstructions even in challenging low-mutation-rate healthy single cells., Competing Interests: The authors declare no competing financial interests., (© 2021 The Authors.)

Microfluidics may revolutionize our ability to write synthetic DNA by addressing several fundamental limitations associated with generating novel genetic constructs. Here we report the first de novo synthesis and cell-free cloning of custom DNA libraries in sub-microliter reaction droplets using programmable digital microfluidics. Specifically, we developed Programmable Order Polymerization (POP), Microfluidic Combinatorial Assembly of DNA (M-CAD) and Microfluidic In-vitro Cloning (MIC) and applied them to de novo synthesis, combinatorial assembly and cell-free cloning of genes, respectively. Proof-of-concept for these methods was demonstrated by programming an autonomous microfluidic system to construct and clone libraries of yeast ribosome binding sites and bacterial Azurine, which were then retrieved in individual droplets and validated. The ability to rapidly and robustly generate designer DNA molecules in an autonomous manner should have wide application in biological research and development., (© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Fundamental aspects of embryonic and post-natal development, including maintenance of the mammalian female germline, are largely unknown. Here we employ a retrospective, phylogenetic-based method for reconstructing cell lineage trees utilizing somatic mutations accumulated in microsatellites, to study female germline dynamics in mice. Reconstructed cell lineage trees can be used to estimate lineage relationships between different cell types, as well as cell depth (number of cell divisions since the zygote). We show that, in the reconstructed mouse cell lineage trees, oocytes form clusters that are separate from hematopoietic and mesenchymal stem cells, both in young and old mice, indicating that these populations belong to distinct lineages. Furthermore, while cumulus cells sampled from different ovarian follicles are distinctly clustered on the reconstructed trees, oocytes from the left and right ovaries are not, suggesting a mixing of their progenitor pools. We also observed an increase in oocyte depth with mouse age, which can be explained either by depth-guided selection of oocytes for ovulation or by post-natal renewal. Overall, our study sheds light on substantial novel aspects of female germline preservation and development., Competing Interests: A patent on the cell lineage analysis method applied in this manuscript has been filed by Yeda Ltd, the licensing arm of the Weizmann Institute.

Bacterial cloning was first introduced over a century ago and has since become one of the most useful procedures in biological research, perhaps paralleled in its ubiquity only by PCR and DNA sequencing. However, unlike PCR and sequencing, cloning has generally remained a manual, labor-intensive, low-throughput procedure. Here we address this issue by developing an automated, computer-aided bacterial cloning method using liquid medium that is based on the principles of (i) limiting dilution of bacteria, (ii) inference of colony forming units (CFUs) based on optical density (OD) readings, and (iii) verification of monoclonality using a mixture of differently colored fluorescently labeled bacteria for transformation. We demonstrate the high-throughput utility of this method by employing it as a cloning platform for a DNA synthesis process.

Dibromochloropropane (DBCP) is an effective nematocide which was shown to suppress spermatogenesis and cause infertility in men and rats exposed to the compound. These damages were described only after 6-8 weeks post injection. The present study was set to detect the early development of the testicular damages. Rats were injected s.c. with DBCP 50 mg/kg. Control animals were injected with the vehicle alone (DMSO). Groups of animals were sacrificed 24 h, 1, 2, 3 and 4 weeks post injection. Body weight of DBCP treated animals was reduced from the second week post injection. Organs' weights of the DBCP treated rats, corrected for differences in body weights, were similar to those of controls. Four weeks post injection testes and accessory gland weights were significantly reduced as compared with controls. Percentage of damaged tubules in the DBCP treated animals were elevated from 16.6 +/- 3.5 at the first day to 70.2 +/- 6.4 at the 4th weeks. Concomitantly with the advance of tubular damage was a reduction in epididymal sperm count in the DBCP treated rats. One week post injection histological changes were evident. These included multinucleated giant cells and tubules blocked with sperm granuloma. It seems that alterations of spermatogenesis appear earlyer and are already noticeable one week post injection.