Clonal differences underlie variable responses to sequential and prolonged treatment.

Cancer cells exhibit dramatic differences in gene expression at the single-cell level, which can predict whether they become resistant to treatment. Treatment perpetuates this heterogeneity, resulting in a diversity of cell states among resistant clones. However, it remains unclear whether these differences lead to distinct responses when another treatment is applied or the same treatment is continued.

Disrupting cellular memory to overcome drug resistance.

Gene expression states persist for varying lengths of time at the single-cell level, a phenomenon known as gene expression memory. When cells switch states, losing memory of their prior state, this transition can occur in the absence of genetic changes. However, we lack robust methods to find regulators of memory or track state switching.

Clonal differences underlie variable responses to sequential and prolonged treatment.

Cancer cells exhibit dramatic differences in gene expression at the single-cell level which can predict whether they become resistant to treatment. Treatment perpetuates this heterogeneity, resulting in a diversity of cell states among resistant clones. However, it remains unclear whether these differences lead to distinct responses when another treatment is applied or the same treatment is continued.

A comprehensive suite of earthquake catalogues for the 2016-2017 Central Italy seismic sequence.

The protracted nature of the 2016-2017 central Italy seismic sequence, with multiple damaging earthquakes spaced over months, presented serious challenges for the duty seismologists and emergency managers as they assimilated the growing sequence to advise the local population. Uncertainty concerning where and when it was safe to occupy vulnerable structures highlighted the need for timely delivery of scientifically based understanding of the evolving hazard and risk. Seismic hazard assessment during complex sequences depends critically on up-to-date earthquake catalogues-i.

Subcellular Detection of SARS-CoV-2 RNA in Human Tissue Reveals Distinct Localization in Alveolar Type 2 Pneumocytes and Alveolar Macrophages.

The widespread coronavirus disease 2019 (COVID-19) is caused by infection with the novel coronavirus SARS-CoV-2. Currently, we have limited understanding of which cells become infected with SARS-CoV-2 in human tissues and where viral RNA localizes on the subcellular level. Here, we present a platform for preparing autopsy tissue for visualizing SARS-CoV-2 RNA using RNA fluorescence in situ hybridization (FISH) with amplification by hybridization chain reaction.

Multiplexed detection of SARS-CoV-2 genomic and subgenomic RNA using hybridization.

The widespread Coronavirus Disease 2019 (COVID-19) is caused by infection with the novel coronavirus SARS-CoV-2. Currently, we have a limited toolset available for visualizing SARS-CoV-2 in cells and tissues, particularly in tissues from patients who died from COVID-19. Generally, single-molecule RNA FISH techniques have shown mixed results in formalin fixed paraffin embedded tissues such as those preserved from human autopsies.

Fragmentation of Small-Cell Lung Cancer Regulatory States in Heterotypic Microenvironments.

Small-cell lung cancers derive from pulmonary neuroendocrine cells, which have stem-like properties to reprogram into other cell types upon lung injury. It is difficult to uncouple transcriptional plasticity of these transformed cells from genetic changes that evolve in primary tumors or secondary metastases. Profiling of single cells is also problematic if the required sample dissociation activates injury-like signaling and reprogramming.

Memory Sequencing Reveals Heritable Single-Cell Gene Expression Programs Associated with Distinct Cellular Behaviors.

Non-genetic factors can cause individual cells to fluctuate substantially in gene expression levels over time. It remains unclear whether these fluctuations can persist for much longer than the time of one cell division. Current methods for measuring gene expression in single cells mostly rely on single time point measurements, making the duration of gene expression fluctuations or cellular memory difficult to measure.

In situ 10-cell RNA sequencing in tissue and tumor biopsy samples.

Single-cell transcriptomic methods classify new and existing cell types very effectively, but alternative approaches are needed to quantify the individual regulatory states of cells in their native tissue context. We combined the tissue preservation and single-cell resolution of laser capture with an improved preamplification procedure enabling RNA sequencing of 10 microdissected cells. This in situ 10-cell RNA sequencing (10cRNA-seq) can exploit fluorescent reporters of cell type in genetically engineered mice and is compatible with freshly cryoembedded clinical biopsies from patients.

Repeating seismic events in China.

About 10% of seismic events in and near China from 1985 to 2000 were repeating events not more than about 1 kilometer from each other. We cross-correlated seismograms from approximately 14,000 earthquakes and explosions and measured relative arrival times to approximately 0.01 second, enabling lateral location precision of about 100 to 300 meters.

ChvD, a chromosomally encoded ATP-binding cassette transporter-homologous protein involved in regulation of virulence gene expression in Agrobacterium tumefaciens.

A yeast two-hybrid screen searching for chromosomally encoded proteins that interact with the Agrobacterium tumefaciens VirB8 protein was carried out. This screen identified an interaction candidate homologous to the partial sequence of a gene that had previously been identified in a transposon screen as a potential regulator of virG expression, chvD. In this report, the cloning of the entire chvD gene is described and the gene is sequenced and characterized.

Nonclassic measles infections in an immune population exposed to measles during a college bus trip.

This study investigated the frequency of mild or asymptomatic measles infections among 44 persons exposed to a student with measles during a 3-day bus trip using two buses. Questionnaires and serum samples were obtained 26-37 days after the trip. All participants had detectable measles-neutralizing antibodies, and none developed classic measles symptoms.

Genomic diversity and differentiation among phytoplasma strains in 16S rRNA groups I (aster yellows and related phytoplasmas) and III (X-disease and related phytoplasmas).

Conserved gene sequences, including 16S rRNA and ribosomal protein gene sequences, were used to evaluate genetic variations in phytoplasma strains belonging to 16S rRNA groups I (aster yellows and related phytoplasmas) and III (X-disease and related phytoplasmas). We used PCR to amplify the sequences of the 16S ribosomal DNA and a segment of the ribosomal protein gene operon (encoding the 3' region of rps19, all of rp122, and rps3) from diverse phytoplasma group I and III strains. Additional chromosomal gene sequences of group I strains were also amplified.

Generation-means analysis and quantitative trait locus mapping of anthracnose stalk rot genes in maize.

A generation-means analysis was performed on two maize populations, each segregating for genes conferring resistance to anthracnose stalk rot (ASR). The populations were derived from a cross of DE811ASR x DE811 and of DE811ASR x LH132. The resistant parent, DE811ASR, was obtained through introgression with MP305 as the donor and DE811 as the recurrent parent.

The adenine phosphoribosyltransferase-encoding gene of Arabidopsis thaliana.

The apt gene, coding for adenine phosphoribosyltransferase (APRT), has been isolated from the plant Arabidopsis thaliana. Data from both Southern analysis and characterization of apt clones isolated from a genomic library is consistent with the occurrence of one apt within the A. thaliana genome.

Sensitive detection and identification of mycoplasma-like organisms in plants by polymerase chain reactions.

DNA amplification by polymerase chain reactions (PCR) was employed to detect host plant infection by several mycoplasmalike organisms (MLOs), including the aster yellows (AY), dwarf aster yellows (DAY), and periwinkle little leaf (0-1) MLOs. For PCR, two pairs of oligonucleotide primers, designated AY18pm and AY19pm, respectively, were synthesized on the basis of partial sequences of cloned AY MLO DNA fragments AY18 and AY19. Reaction mixtures containing primer pair AY18pm yielded a DNA product of 1.

Mouse transgenes in human cells detect specific base substitutions.

We describe a system of transgenic human cell lines that detects and identifies specific point mutations at defined positions within a gene. The target transgenome is a mouse adenine phosphoribosyltransferase (APRT) gene rendered nonfunctional by introduction of a substitution at either of two bases that comprise a splice acceptor site. Reversion at a mutated site results in the expression of wild-type mouse APRT and consequent growth of APRT+ transgenic cell colonies.

Denaturing gradient gel analysis of single-base substitutions at a mouse adenine phosphoribosyltransferase splice acceptor site.

Denaturing gradient gel electrophoresis (DGGE) can detect single-base changes in DNA. We used site-directed mutagenesis to produce all six possible single-base substitutions at a splice acceptor consensus AG dinucleotide within the mouse adenine phosphoribosyltransferase (aprt) gene. Studies of mouse and Chinese hamster cell aprt indicate a high level of both spontaneous and induced mutations in this region.

Identification of DNA sequences required for mouse APRT gene expression.

The mouse aprt promoter contains four GC boxes, which bind transcription factor Spl in vitro, and lacks both TATA and CCAAT boxes. Removal of the two most distal GC boxes of this promoter had little effect on APRT enzyme levels produced in a transient expression assay. Deletion of the distal three GC boxes resulted in a 50% reduction, and deletion of all GC boxes resulted in essentially complete loss of APRT activity.

Computational procedure for a weighted diallel analysis.

A diallel analysis is described for the case in which the values of the characteristic used in an inheritance study have unequal variances. Such a characteristic can be a mean, a slope of a regression line, or the estimates of some parameter of a linear or nonlinear model. Computational formulae are presented which incorporate the necessary weighting along with the statistics of the Hayman-Jinks method for diallel analysis.

Comparative anatomy of the human APRT gene and enzyme: nucleotide sequence divergence and conservation of a nonrandom CpG dinucleotide arrangement.

The functional human adenine phosphoribosyltransferase (APRT) gene is less than 2.6 kilobases in length and contains five exons. The amino acid sequences of APRTs have been highly conserved throughout evolution.