Probabilistic approaches for investigating species co-occurrence from presence-absence maps.

Background: In this research, we propose probabilistic approaches to identify pairwise patterns of species co-occurrence by using presence-absence maps only. In particular, the two-by-two contingency table constructed from a presence-absence map of two species would be sufficient to compute the test statistics and perform the statistical tests proposed in this article. Some previous studies have investigated species co-occurrence through incidence data of different survey sites. We focus on using presence-absence maps for a specific study plot instead. The proposed methods are assessed by a thorough simulation study. Methods: A Chi-squared test is used to determine whether the distributions of two species are independent. If the null hypothesis of independence is rejected, the Chi-squared method can not distinguish positive or negative association between two species. We propose six different approaches based on either the binomial or Poisson distribution to obtain p-values for testing the positive (or negative) association between two species. When we test to investigate a positive (or negative) association, if the p-value is below the predetermined level of significance, then we have enough evidence to support that the two species are positively (or negatively) associated. Results: A simulation study is conducted to demonstrate the type-I errors and the testing powers of our approaches. The probabilistic approach proposed by Veech (2013) is served as a benchmark for comparison. The results show that the type-I error of the Chi-squared test is close to the significance level when the presence rate is between 40% and 80%. For extremely low or high presence rate data, one of our approaches outperforms Veech (2013)'s in terms of the testing power and type-I error rate. The proposed methods are applied to a tree data of Barro Colorado Island in Panama and a tree data of Lansing Woods in USA. Both positive and negative associations are found among some species in these two real data.

Tailor-made three-dimensional printing vaginal pessary to treat pelvic organ prolapse: a pilot study.

OBJECTIVE: This study aimed to apply three-dimensional (3D) printing technology to treat women with pelvic organ prolapse (POP) and to evaluate efficacy based on the improvement by quality of life (QOL) questionnaires. METHODS: This was a pilot study at a tertiary urogynecology unit in Taiwan. Between January 2021 and June 6, 2021, participants who opted for self-management using Gellhorn pessaries to treat symptomatic POP were enrolled. For each woman, the original Gellhorn pessary was placed into the vagina to restore the prolapsed tissues and under transvaginal ultrasound guided to evaluate the gap which the Gellhorn pessary cannot cover. Otoform (an impression silicone) was used to make a model and have it hooked onto Gellhorn pessary (template). We collected templates and then applied 3D printing to customize the silicone vaginal pessary. All women completed multiple validated QOL questionnaires at baseline and at 3 and 6 months. RESULTS: Six women completed the study. The QOL questionnaires revealed significant improvements across the board. CONCLUSIONS: Our study demonstrates that a tailor made 3D pessary can be used for women with POP. A customized pessary can be made with the help of transvaginal ultrasound and 3D printing technology.

Combining CRISPR and CRISPRi Systems for Metabolic Engineering of E. coli and 1,4-BDO Biosynthesis.

Biosynthesis of 1,4-butanediol (1,4-BDO) in E. coli requires an artificial pathway that involves six genes and time-consuming, iterative genome engineering. CRISPR is an effective gene editing tool, while CRISPR interference (CRISPRi) is repurposed for programmable gene suppression. This study aimed to combine both CRISPR and CRISPRi for metabolic engineering of E. coli and 1,4-BDO production. We first exploited CRISPR to perform point mutation of gltA, replacement of native lpdA with heterologous lpdA, knockout of sad and knock-in of two large (6.0 and 6.3 kb in length) gene cassettes encoding the six genes (cat1, sucD, 4hbd, cat2, bld, bdh) in the 1,4-BDO biosynthesis pathway. The successive E. coli engineering enabled production of 1,4-BDO to a titer of 0.9 g/L in 48 h. By combining the CRISPRi system to simultaneously suppress competing genes that divert the flux from the 1,4-BDO biosynthesis pathway (gabD, ybgC and tesB) for >85%, we further enhanced the 1,4-BDO titer for 100% to 1.8 g/L while reducing the titers of byproducts gamma-butyrolactone and succinate for 55% and 83%, respectively. These data demonstrate the potential of combining CRISPR and CRISPRi for genome engineering and metabolic flux regulation in microorganisms such as E. coli and production of chemicals (e.g., 1,4-BDO).

CRISPR interference (CRISPRi) for gene regulation and succinate production in cyanobacterium S. elongatus PCC 7942.

BACKGROUND: Cyanobacterium Synechococcus elongatus PCC 7942 holds promise for biochemical conversion, but gene deletion in PCC 7942 is time-consuming and may be lethal to cells. CRISPR interference (CRISPRi) is an emerging technology that exploits the catalytically inactive Cas9 (dCas9) and single guide RNA (sgRNA) to repress sequence-specific genes without the need of gene knockout, and is repurposed to rewire metabolic networks in various procaryotic cells. RESULTS: To employ CRISPRi for the manipulation of gene network in PCC 7942, we integrated the cassettes expressing enhanced yellow fluorescent protein (EYFP), dCas9 and sgRNA targeting different regions on eyfp into the PCC 7942 chromosome. Co-expression of dCas9 and sgRNA conferred effective and stable suppression of EYFP production at efficiencies exceeding 99%, without impairing cell growth. We next integrated the dCas9 and sgRNA targeting endogenous genes essential for glycogen accumulation (glgc) and succinate conversion to fumarate (sdhA and sdhB). Transcription levels of glgc, sdhA and sdhB were effectively suppressed with efficiencies depending on the sgRNA binding site. Targeted suppression of glgc reduced the expression to 6.2%, attenuated the glycogen accumulation to 4.8% and significantly enhanced the succinate titer. Targeting sdhA or sdhB also effectively downregulated the gene expression and enhanced the succinate titer ≈12.5-fold to ≈0.58-0.63 mg/L. CONCLUSIONS: These data demonstrated that CRISPRi-mediated gene suppression allowed for re-directing the cellular carbon flow, thus paving a new avenue to rationally fine-tune the metabolic pathways in PCC 7942 for the production of biotechnological products.

CRISPR-Cas9 for the genome engineering of cyanobacteria and succinate production.

Cyanobacteria hold promise as a cell factory for producing biofuels and bio-derived chemicals, but genome engineering of cyanobacteria such as Synechococcus elongatus PCC 7942 poses challenges because of their oligoploidy nature and long-term instability of the introduced gene. CRISPR-Cas9 is a newly developed RNA-guided genome editing system, yet its application for cyanobacteria engineering has yet to be reported. Here we demonstrated that CRISPR-Cas9 system can effectively trigger programmable double strand break (DSB) at the chromosome of PCC 7942 and provoke cell death. With the co-transformation of template plasmid harboring the gene cassette and flanking homology arms, CRISPR-Cas9-mediated DSB enabled precise gene integration, ameliorated the homologous recombination efficiency and allowed the use of lower amount of template DNA and shorter homology arms. The CRISPR-Cas9-induced cell death imposed selective pressure and enhanced the chance of concomitant integration of gene cassettes into all chromosomes of PCC 7942, hence accelerating the process of obtaining homogeneous and stable recombinant strains. We further explored the feasibility of engineering cyanobacteria by CRISPR-Cas9-assisted simultaneous glgc knock-out and gltA/ppc knock-in, which improved the succinate titer to 435.0±35.0µg/L, an ≈11-fold increase when compared with that of the wild-type cells. These data altogether justify the use of CRISPR-Cas9 for genome engineering and manipulation of metabolic pathways in cyanobacteria.

The transactivation domain of heterogeneous nuclear ribonucleoprotein K overlaps its nuclear shuttling domain.

The heterogeneous nuclear ribonucleoprotein K (hnRNP K) protein is a versatile molecule that interacts with RNA, DNA, and a number of transcription factors, implicating it in transcription, splicing, and translation processes. The underlying mechanism of transcription stimulation by hnRNP K is not well understood. To explore the possibility of a putative transactivation activity of hnRNP K, we produced constructs in which the yeast Gal4 DNA-binding domain was fused to various hnRNP K fragments in one-hybrid mammalian cells. Our results reveal that the K nuclear shuttling (KNS) domain, a well-known signal for nuclear import and export, is also responsible for the transactivation activity of hnRNP K protein. Importin alpha and beta proteins are involved in the regulation of the transactivation activity of the KNS domain via their competition for the nuclear pore complex. Site-directed mutants of serine residue 353 to alanine or aspartic acid or a series of truncated mutants of amino acids 338-363 of hnRNP K suggest the transactivation activity of KNS is primarily dependent on its amino acid composition and intact structure. Our results suggest that endogenous p53 is not required for the activity of the KNS domain, but that overexpression of exogenous p53 might affect its activity in a dose-dependent manner. We thus demonstrate the existence of a strong transactivation domain in hnRNP K and define the regulatory mechanism involved in its protein-protein interaction within the KNS domain in cells.