Tailoring p-Type Behavior in ZnO Quantum Dots through Enhanced Sol-Gel Synthesis: Mechanistic Insights into Zinc Vacancies

The synthesis and control of properties of p-type ZnO is crucial for a variety of optoelectronic and spintronic applications; however, it remains challenging due to the control of intrinsic midgap (defect) states. In this study, we demonstrate a synthetic route to yield colloidal ZnO quantum dots (QD) via an enhanced sol-gel process that effectively eliminates the residual intermediate reaction molecules, which would otherwise weaken the excitonic emission. This process supports the creation of ZnO with p-type properties or compensation of inherited n-type defects, primarily due to zinc vacancies under oxygen-rich conditions. The in-depth analysis of carrier recombination in the midgap across several time scales reveals microsecond carrier lifetimes at room temperature which are expected to occur via zinc vacancy defects, supporting the promoted p-type character of the synthesized ZnO QDs.

Accessing metal-specific orbital interactions in C-H activation with resonant inelastic X-ray scattering

Photochemically prepared transition-metal complexes are known to be effective at cleaving the strong C-H bonds of organic molecules in room temperature solutions. There is also ample theoretical evidence that the two-way, metal to ligand (MLCT) and ligand to metal (LMCT), charge-transfer between an incoming alkane C-H group and the transition metal is the decisive interaction in the C-H activation reaction. What is missing, however, are experimental methods to directly probe these interactions in order to reveal what determines reactivity of intermediates and the rate of the reaction. Here, using quantum chemical simulations we predict and propose future time-resolved valence-to-core resonant inelastic X-ray scattering (VtC-RIXS) experiments at the transition metal L-edge as a method to provide a full account of the evolution of metal-alkane interactions during transition-metal mediated C-H activation reactions. For the model system cyclopentadienyl rhodium dicarbonyl (CpRh(CO)2), we demonstrate, by simulating the VtC-RIXS signatures of key intermediates in the C-H activation pathway, how the Rh-centered valence-excited states accessible through VtC-RIXS directly reflect changes in donation and back-donation between the alkane C-H group and the transition metal as the reaction proceeds via those intermediates. We benchmark and validate our quantum chemical simulations against experimental steady-state measurements of CpRh(CO)2 and Rh(acac)(CO)2 (where acac is acetylacetonate). Our study constitutes the first step towards establishing VtC-RIXS as a new experimental observable for probing reactivity of C-H activation reactions. More generally, the study further motivates the use of time-resolved VtC-RIXS to follow the valence electronic structure evolution along photochemical, photoinitiated and photocatalytic reactions with transition metal complexes.

Dosimetric comparison of free-breathing versus respiratory motion-managed radiotherapy via four-dimensional computed tomography-based volumetric-modulated arctherapy for lung cancer

PURPOSE

The aim of this study is to use respiratory motion-managed radiotherapy (RT) to reduce side effects and to compare dosimetric factors with free-breathing planning in patients with lung cancer.

MATERIALS AND METHODS

Simulation images were obtained in 10 respiratory phases with free breathing using four-dimensional computed tomography (4D-CT) scanner. Planning target volume (PTV) was created with 5mm margins in each direction of the internal target volume delineated using the maximum intensity projection. A volumetric arc treatment (VMAT) plan was created so that the prescribed dose would cover 98% of the PTV. Target volumes for the free-breathing VMAT plan were created according to ICRU Reports 62 and the same prescribed dose was used.

RESULTS

Patients were evaluated during January 2020. Median 63Gy (59.4-64) RT was administered. Median PTV volumes were 173.53 and 494.50cm3 (P=0.008) and dose covering 95% of PTV volume was 62.97 and 60.51Gy (P=0.13) in 4D-CT based and free-breathing VMAT plans, respectively. The mean and V50 heart dose was 6.03Gy (vs. 10.36Gy, P=0.043) and 8.2% (vs. 33.9%, P=0.007), and significantly lower in 4D-CT based VMAT plans and there was also found a non-significant reduction for other risky organ doses.

CONCLUSION

Ten patients treated with respiratory motion-managed RT with 4D-CT based VMAT technique. It was observed that PTV did not increase, the target was covered with 95% accuracy, and with statistical significance in heart doses, all risky organ doses were found to be less.

Assessment of quantitative zonal parameters of prostate gland in discrimination of normal, benign, and malignant conditions: are these the more reliable parameters in the diagnosis of prostate cancer?

OBJECTIVE

Prostate cancer diagnosis and treatment are increasing in current public healthcare programs. An improved resolution multiparametric magnetic resonance imaging (MRI) has shown the potential to enhance the detection and differentiation of this medical condition. In this study, MR perfusion parameters were investigated in different ages and diseases to differentiate clinically significant prostate cancer.

PATIENTS AND METHODS

From January 2017 to December 2022, 72 consecutive patients, who had undergone multiparametric MR imaging were enrolled in this study. Four different patient groups were formed: (1) those with prostate cancer, (2) those with prostatitis, (3) those with benign prostate hyperplasia (BPH), and (4) a control group. Quantitative dynamic contrast-enhanced (DCE)-MRI pharmacokinetic parameters included Ktrans, Kep, Ve, and iAUG. Different measurements were obtained from both the peripheral and transitional zones (PZ and TZ, respectively). Means values were compared between groups based on a univariate analysis.

RESULTS

Ktrans and Kep values in the PZ were found to be statistically significantly lower in the control group (p = 0. 003 and p = 0. 011, respectively). It was seen that Ktrans and Ve measurements obtained from PZ had a statistically significant determinant in detecting malignancy (p = 0. 013 and p = 0. 036, respectively). It was seen that Ktrans, Ve, and iAUG obtained from the TZ showed a statistically significant difference in prostate cancer (p = 0.025, p = 0.005, and p = 0. 011, respectively) in contrast to other cases. Peripheral Ve values were statistically significantly lower than those measured Ve values from the TZ in prostate cancer cases (p = 0.002) in contrast to the other cases.

CONCLUSIONS

Quantitative DCE-MRI parameters may vary according to age, disease, and zonal anatomy. These differences may contribute to the diagnosis of clinically relevant prostate cancer.

The complete chloroplast genome of Cicer reticulatum and comparative analysis against relative Cicer species

The chloroplast (cp) genome is an adequate genomic resource to investigate evolutionary relationships among plant species and it carries marker genes available for species identification. The Cicer reticulatum is one of perennial species as the progenitor of cultivated chickpeas. Although a large part of the land plants has a quadruple chloroplast genome organization, the cp genome of C. reticulatum consists of one LSC (Large Single Copy Region), one SSC (Small Single Copy Region), and one IR (Inverted Repeat) region, which indicates that it has an untypical and unique structure. This type of chloroplast genome belongs to the IR-lacking clade. Chloroplast DNA (cpDNA) was extracted from fresh leaves using a high salt-based protocol and sequencing was performed using DNA Nanoball Sequencing technology. The comparative analysis employed between the species to examine genomic differences and gene homology. The study also included codon usage frequency analysis, hotspot divergence analysis, and phylogenetic analysis using various bioinformatics tools. The cp genome of C. reticulatum was found 125,794 bp in length, with an overall GC content of 33.9%. With a total of 79 protein-coding genes, 34 tRNA genes, and 4 rRNA genes. Comparative genomic analysis revealed 99.93% similarity between C. reticulatum and C. arietinum. Phylogenetic analysis further indicated that the closest evolutionary relative to C. arietinum was C. reticulatum, whereas the previously sequenced wild Cicer species displayed slight distinctions across their entire coding regions. Several genomic regions, such as clpP and ycf1, were found to exhibit high nucleotide diversity, suggesting their potential utility as markers for investigating the evolutionary relationships within the Cicer genus. The first complete cp genome sequence of C. reticulatum will provide novel insights for future genetic research on Cicer crops.

Ex Vivo Drug Testing in Patient-derived Papillary Renal Cancer Cells Reveals EGFR and the BCL2 Family as Therapeutic Targets

BACKGROUND

Immune checkpoint inhibitors and antiangiogenic agents are used for first-line treatment of advanced papillary renal cell carcinoma (pRCC) but pRCC response rates to these therapies are low.

OBJECTIVE

To generate and characterise a functional ex vivo model to identify novel treatment options in advanced pRCC.

DESIGN, SETTING, AND PARTICIPANTS

We established patient-derived cell cultures (PDCs) from seven pRCC samples from patients and characterised them via genomic analysis and drug profiling.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

Comprehensive molecular characterisation in terms of copy number analysis and whole-exome sequencing confirmed the concordance of pRCC PDCs with the original tumours. We evaluated their sensitivity to novel drugs by generating drug scores for each PDC.

RESULTS AND LIMITATIONS

PDCs confirmed pRCC-specific copy number variations such as gains in chromosomes 7, 16, and 17. Whole-exome sequencing revealed that PDCs retained mutations in pRCC-specific driver genes. We performed drug screening with 526 novel and oncological compounds. Whereas exposure to conventional drugs showed low efficacy, the results highlighted EGFR and BCL2 family inhibition as the most effective targets in our pRCC PDCs.

CONCLUSIONS

High-throughput drug testing on newly established pRCC PDCs revealed that inhibition of EGFR and BCL2 family members could be a therapeutic strategy in pRCC.

PATIENT SUMMARY

We used a new approach to generate patient-derived cells from a specific type of kidney cancer. We showed that these cells have the same genetic background as the original tumour and can be used as models to study novel treatment options for this type of kidney cancer.

First report of Ascochyta rabiei infections on endemic Turkish populations of Cicer bijugum and C. turcicum

Ascochyta rabiei causes Ascochyta blight disease on C. arietinum as well as on annual C. reticulatum, C. pinnatifidum and C. judaicum and perennial C. montbretii, C. isauricum, C. ervoides species (Can et al. 2007; Frenkel et al. 2007; Ozkilinc et al. 2019; Peever et al. 2007; Tekin et al. 2018). During field survey studies carried out on annual Cicer spp. in June 2022, concentric ring-shaped lesions were observed on the stems and leaves of C. bijugum in Mardin province and C. turcicum in Elazig province. Cicer reticulatum and C. arietinum plants were also found in the location where C. bijugum was found. No disease symptoms were observed in other Cicer species, while C. bijugum had 32% disease incidence. The disease incidence among the C. turcicum population was 37.3 %, and no chickpea cultivation area was found near it. Diseased plant parts were surface sterilized, placed on ½ potato dextrose agar (PDA) and incubated at 24±2 oC in 12 hours light/dark photoperiod. Each symptomatic plant was considered as one isolate. Monosporic isolates were obtained and the same colony morphology developed from all plant parts of C. turcicum and C. bijugum. Spores were oblong and spore sizes were 10.73±0.62 µm (n=15) in length and 3.60±0.25 (n=15) µm in width, 10.64±0.98 (n=15) µm in length and 3.00±0.26 (n=15) µm in width for isolates obtained from C. turcicum and C. bijugum, respectively. Amplicons for all 40 isolates were generated with mating type (MAT) primers, and the ITS region was amplified and sequenced by using the ITS4 and ITS5 primers (Peever et al. 2007). For the MAT primers, a 700 bp amplicon was observed for all the 20 isolates obtained from C. bijugum conferring to MAT1.1 idiomorph. In contrast, for the isolates obtained from C. turcicum 14 isolates had a 700 bp amplicon for MAT1.1 and 6 isolates had a 500 bp amplicon for MAT1.2, thus representing both idiomorphs in a ~2:1 ratio. BLAST analysis of the ITS sequences showed 100% homology with the reference ITS sequences for A. rabiei except for 23 SVRC CT 09/22 and 23 SVRC CT 22/22 isolates showing 99.81 % similarity. All sequences were submitted to GenBank (OP967923, OP967924, OP967925, OP967926 and OP967927 for A. rabiei isolates from C. turcicum; OP981072, OP981073 and OP981074 for A. rabiei isolates from C. bijugum). A phylogenetic tree was constructed using MEGAX software and the Neighbor-Joining method, using the ITS sequences of A. rabiei, other Ascochyta spp. and Colletotrichum gloeosporioides. The A. rabiei isolates from C. turcicum and C. bijugum clustered together with A. rabiei sequences from the NCBI (Kumar et al. 2018). Twelve-day-old C. bijugum and C. turcicum seedlings were inoculated with 5 x 105 spore/mL concentration of spores from 5 C. turcicum and 3 C. bijugum isolates and put in plastic bags for 24 hours (Can et al. 2007). Pathogenicity tests were carried out in triplicate pots with four plants each for each isolate in a controlled climate chamber at 24±2 oC, 70% humidity under 12 hours light/dark conditions. The first symptoms were observed within 7 days after inoculation (dai) and severe Ascochyta blight symptoms developed on all plants by 21 dai. Cicer bijugum and C. turcicum are endemic Cicer species exhibiting narrow distribution in the Southeastern region of Republic of Türkiye. As a major biotic stress source, A. rabiei could be an important threat to Cicer spp (Abbo et al. 2003). To our knowledge, this is the first report of A. rabiei from C. bijugum and C. turcicum species.

Tracking C-H activation with orbital resolution

Transition metal reactivity toward carbon-hydrogen (C-H) bonds hinges on the interplay of electron donation and withdrawal at the metal center. Manipulating this reactivity in a controlled way is difficult because the hypothesized metal-alkane charge-transfer interactions are challenging to access experimentally. Using time-resolved x-ray spectroscopy, we track the charge-transfer interactions during C-H activation of octane by a cyclopentadienyl rhodium carbonyl complex. Changes in oxidation state as well as valence-orbital energies and character emerge in the data on a femtosecond to nanosecond timescale. The x-ray spectroscopic signatures reflect how alkane-to-metal donation determines metal-alkane complex stability and how metal-to-alkane back-donation facilitates C-H bond cleavage by oxidative addition. The ability to dissect charge-transfer interactions on an orbital level provides opportunities for manipulating C-H reactivity at transition metals.

ROS Induction Targets Persister Cancer Cells with Low Metabolic Activity in NRAS-Mutated Melanoma

Clinical management of melanomas with NRAS mutations is challenging. Targeting MAPK signaling is only beneficial to a small subset of patients due to resistance that arises through genetic, transcriptional, and metabolic adaptation. Identification of targetable vulnerabilities in NRAS-mutated melanoma could help improve patient treatment. Here, we used multiomics analyses to reveal that NRAS-mutated melanoma cells adopt a mesenchymal phenotype with a quiescent metabolic program to resist cellular stress induced by MEK inhibition. The metabolic alterations elevated baseline reactive oxygen species (ROS) levels, leading these cells to become highly sensitive to ROS induction. In vivo xenograft experiments and single-cell RNA sequencing demonstrated that intratumor heterogeneity necessitates the combination of a ROS inducer and a MEK inhibitor to inhibit both tumor growth and metastasis. Ex vivo pharmacoscopy of 62 human metastatic melanomas confirmed that MEK inhibitor-resistant tumors significantly benefited from the combination therapy. Finally, oxidative stress response and translational suppression corresponded with ROS-inducer sensitivity in 486 cancer cell lines, independent of cancer type. These findings link transcriptional plasticity to a metabolic phenotype that can be inhibited by ROS inducers in melanoma and other cancers.

SIGNIFICANCE

Metabolic reprogramming in drug-resistant NRAS-mutated melanoma cells confers sensitivity to ROS induction, which suppresses tumor growth and metastasis in combination with MAPK pathway inhibitors.

Unravelling homologous recombination repair deficiency and therapeutic opportunities in soft tissue and bone sarcoma

Defects in homologous recombination repair (HRR) in tumors correlate with poor prognosis and metastases development. Determining HRR deficiency (HRD) is of major clinical relevance as it is associated with therapeutic vulnerabilities and remains poorly investigated in sarcoma. Here, we show that specific sarcoma entities exhibit high levels of genomic instability signatures and molecular alterations in HRR genes, while harboring a complex pattern of chromosomal instability. Furthermore, sarcomas carrying HRDness traits exhibit a distinct SARC-HRD transcriptional signature that predicts PARP inhibitor sensitivity in patient-derived sarcoma cells. Concomitantly, HRD^high sarcoma cells lack RAD51 nuclear foci formation upon DNA damage, further evidencing defects in HRR. We further identify the WEE1 kinase as a therapeutic vulnerability for sarcomas with HRDness and demonstrate the clinical benefit of combining DNA damaging agents and inhibitors of DNA repair pathways ex vivo and in the clinic. In summary, we provide a personalized oncological approach to treat sarcoma patients successfully.

Orthopedic Management of Radial Tunnel Syndrome: A Diagnostic and Treatment Dilemma

OBJECTIVE

The first-line treatment for radial tunnel syndrome is conservative despite limited evidence concerning its efficiency. Surgical release is indicated if nonsurgical measures fail. Radial tunnel syndrome cases may be misdiagnosed as the more common lateral epicondylitis, and misdiagnosing radial tunnel syndrome causes wrong treatment and, thus, the perpetuation or increase of the pain. Although radial tunnel syndrome is a rare disorder, such cases can be encountered in tertiary hand surgery centers. This study aimed to present our experience in diagnosing and managing patients with radial tunnel syndrome.

MATERIAL AND METHODS

Eighteen patients (7 male, 11 female; mean age=41.5 years, age range=22-61) in whom radial tunnel syndrome was diagnosed and treated at a single tertiary care center were retrospectively reviewed and included. Previous diagnoses (wrong diagnosis, delayed diagnosis, missed diagnosis, and other), previous treatments for such diagnoses, and their results before presenting to our institution were recorded. The shortened disabilities of the arm, shoulder, and hand questionnaire score and visual analog scale score were recorded before the surgery and at the final follow-up appointment.

RESULTS

All the patients included in the study underwent steroid injections. Eleven patients (11/18, 61%) benefited from steroid injection and conservative treatment. The remaining 7 patients refractory to conservative treatment were offered surgical treatment. Of these, 6 patients accepted surgery while 1 did not accept it. In all patients, the mean visual analog scale score significantly improved from 6.38 (range: 5-8) to 2.1 (range: 0-7) (P < .001). The mean quick-disabilities of the arm, shoulder, and hand questionnaire scores were significantly improved from 43.4 (range: 31.8-52.5) preoperatively to 8.7 (range: 0-45.5) at the final follow-up (P < .001). In the surgical treatment group, the mean visual analog scale score significantly improved from 6.1 (range: 5-7) to 1.2 (range: 0-4) (P < .001). The mean quick-disabilities of the arm, shoulder, and hand questionnaire scores were significantly improved from 37.4 (range: 31.2-45.5) preoperatively to 4.7 (range: 0-13.6) at the final follow-up (P < .001).

CONCLUSION

Our experience has shown that satisfactory results can be obtained by surgical treatment for patients with radial tunnel syndrome refractory to nonsurgical treatment whose diagnosis is confirmed by a thorough physical examination.

CanIsoNet: a database to study the functional impact of isoform switching events in diseases

Motivation

Alternative splicing, as an essential regulatory mechanism in normal mammalian cells, is frequently disturbed in cancer and other diseases. Switches in the expression of most dominant alternative isoforms can alter protein interaction networks of associated genes giving rise to disease and disease progression. Here, we present CanIsoNet, a database to view, browse and search isoform switching events in diseases. CanIsoNet is the first webserver that incorporates isoform expression data with STRING interaction networks and ClinVar annotations to predict the pathogenic impact of isoform switching events in various diseases.

Results

Data in CanIsoNet can be browsed by disease or searched by genes or isoforms in annotation-rich data tables. Various annotations for 11 811 isoforms and 14 357 unique isoform switching events across 31 different disease types are available. The network density score for each disease-specific isoform, PFAM domain IDs of disrupted interactions, domain structure visualization of transcripts and expression data of switched isoforms for each sample is given. Additionally, the genes annotated in ClinVar are highlighted in interactive interaction networks.

Availability and implementation

CanIsoNet is freely available at https://www.caniso.net. The source codes can be found under a Creative Common License at https://github.com/kahramanlab/CanIsoNet_Web.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

ROS1 genomic rearrangements are rare actionable drivers in microsatellite stable colorectal cancer

c-Ros oncogene 1, receptor tyrosine kinase (ROS1) genomic rearrangements have been reported previously in rare cases of colorectal cancer (CRC), yet little is known about the frequency, molecular characteristics, and therapeutic vulnerabilities of ROS1-driven CRC. We analyzed a clinical dataset of 40 589 patients with CRC for ROS1 genomic rearrangements and their associated genomic characteristics (Foundation Medicine, Inc [FMI]). We moreover report the disease course and treatment response of an index patient with ROS1-rearranged metastatic CRC. ROS1 genomic rearrangements were identified in 34 (0.08%) CRC samples. GOPC-ROS1 was the most common ROS1 fusion identified (11 samples), followed by TTC28-ROS1 (3 samples). Four novel 5' gene partners of ROS1 were identified (MCM9, SRPK1, EPHA6, P4HA1). Contrary to previous reports on fusion-positive CRC, ROS1-rearrangements were found exclusively in microsatellite stable (MSS) CRCs. KRAS mutations were significantly less abundant in ROS1-rearranged vs ROS1 wild type cases. The index patient presented with chemotherapy-refractory metastatic right-sided colon cancer harboring GOPC-ROS1. Molecularly targeted treatment with crizotinib induced a rapid and sustained partial response. After 15 months on crizotinib disseminated tumor progression occurred and KRAS Q61H emerged in tissue and liquid biopsies. ROS1 rearrangements define a small, yet therapeutically actionable molecular subgroup of MSS CRC. In summary, the high prevalence of GOPC-ROS1 and noncanonical ROS1 fusions pose diagnostic challenges. We advocate NGS-based comprehensive molecular profiling of MSS CRCs that are wild type for RAS and BRAF and patient enrollment in precision trials.

Endometrial carcinoma detection with 3.0 Tesla imaging: which sequence is more useful

OBJECTIVE

Detection of endometrial cancer (EC) is crucial in pre-operative EC management. The study aimed at determining the most reliable sequence in magnetic resonance imaging (MRI) evaluation at the EC. Different sequences were compared using histopathological results as the gold standard.

PATIENTS AND METHODS

In this retrospective study, 62 women diagnosed with EC were examined using 3 Tesla MR and post-hysterectomy histopathological examination. The MRI protocol included diffusion-weighted imaging (DWI), T2 weighted images, Dynamic Contrast T1 weighted images, and ZOOMit DWI. Apparent diffusion coefficient (ADC) maps were also obtained. ADC maps were calculated for both DWI and ZOOMit DWI. All serial images were analyzed by endometrial distance to account for myometrial invasion and tumor size. All sequences and histopathological results were compared using the paired sample t-test.

RESULTS

In all 32 women, post-hysterectomy histopathological confirmation was obtained. Mean myometrial invasion values were not significantly different after comparing DWI, ZOOM it DWI, and Dynamic contrast enhancement (DCE)-T1WI (p=0.054, p=0.039). The first strong correlation was found between DWI and ZOOMit DWI (0.943). The second was between ZOOMit DWI and DCE-T1 WI (0.949). Comparing each set of sequences, no statistically significant differences in tumor size (p > 0.05) were found. Also, no statistically significant differences between images and histopathological size were found. The ADC values of ZOOMit DWI indicated that this method detected significant differences between EC histological subtypes.

CONCLUSIONS

Each sequence is essential and valuable, whereas priorities may vary depending on the desired information. The most valuable sequences for the myometrial invasion were ZOOMit and conventional DWI. T2WI and DCE T1 WI were more valuable sequences the size of EC.

MTPpilot: An Interactive Software for Visualization of Next-Generation Sequencing Results in Molecular Tumor Boards

Comprehensive targeted next-generation sequencing (NGS) panels are routinely used in modern molecular cancer diagnostics. In molecular tumor boards, the detected genomic alterations are often discussed to decide the next treatment options for patients with cancer. With the increasing size and complexity of NGS panels, the discussion of these results becomes increasingly complex, especially if they are reported in a text-based form, as it is the standard in current molecular pathology.

The Complete Chloroplast Genome Sequence of Cicer bijugum, Genome Organization and Comparison with Related Species

Background

Chickpea is one of Turkey's most significant legumes, and because of its high nutritional value, it is frequently preferred in human nourishment.Chloroplasts, which have their own genetic material, are organelles responsible for photosynthesis in plant cells and their genome contains non-trivial information about the molecular features and evolutionary process of plants.

Objective

Current study aimed at revealing complete chloroplast genome sequence of one of the wild type Cicer species, Cicer bijugum, and comparing its genome with cultivated Cicer species, Cicer arietinum, by using bioinformatics analysis tools. Except for Cicer arietinum, there has been no study on the chloroplast genome sequence of Cicer species.Therefore, we targeted to reveal the complete chloroplast genome sequence of wild type Cicer species, Cicer bijugum, and compare the chloroplast genome of Cicer bijugum with the cultivated one Cicer arietinum.

Methods

In this study, we sequenced the whole chloroplast genome of Cicer bijugum, one of the wild types of chickpea species, with the help Next Generation Sequencing platform and compared it with the chloroplast genome of the cultivated chickpea species, Cicer arietinum, by using online bioinformatics analysis tools.

Results

We determined the size of the chloroplast genome of C. bijugum as 124,804 bp and found that C. bijugum did not contain an inverted repeat region in its chloroplast genome. Comparative analysis of the C. bijugum chloroplast genome uncovered thirteen hotspot regions (psbA, matK, rpoB, rpoC1, rpoC2, psbI, psbK, accD, rps19, ycf2, ycf1, rps15, and ndhF) and seven of them (matK, accD, rps19, ycf1, ycf2, rps15 and ndhF) could potentially be used as strong molecular markers for species identification. It has been determined that C. bijugum was phylogenetically closer to cultivated chickpea as compared to the other species.

Conclusion

It is aimed that the data obtained from this study, which is the first study in which whole chloroplast genomes of wild chickpea species were sequenced, will guide researchers in future molecular, evolutionary, and genetic engineering studies with chickpea species.

Frequency, molecular characteristics, and therapeutic targeting of ROS1 oncogenic fusions in colorectal cancer

160

Background: c-Ros oncogene 1, receptor tyrosine kinase ( ROS1) rearrangements have been reported in colorectal cancer (CRC), but little is known about the molecular and clinical features of ROS1-driven CRC and the response to ROS1-targeted treatment in CRC patients. Methods: We report disease course and treatment response of an index patient with chemotherapy-refractory right-sided metastatic CRC, harboring an activating ROS1 fusion ( GOPC-ROS1). Moreover, we examined 40,589 patients with CRC who underwent comprehensive genomic profiling as part of routine clinical care at Foundation Medicine (Cambridge, MA); all classes of alterations in at least 324 genes were assessed, including ROS1. Results: The index patient experienced a rapid and sustained partial response to molecularly targeted treatment with crizotinib. After 15 months on crizotinib, disseminated tumor progression occurred, with KRAS Q61H emerging in tumor tissue (53.7% variant allele frequency (VAF)) and liquid biopsy (13.5% VAF). Within the clinical cohort, ROS1 genomic rearrangements ( ROS1 RE (+)) were identified in 34 out of 40,589 (0.08%) CRC samples. GOPC-ROS1 was the most commonly identified ROS1 fusion (11/34 samples), followed by TTC28-ROS1 (3/34 samples). All ROS1-alterations were found in microsatellite-stable (MSS) CRCs, and ROS1 genomic alterations were significantly enriched in KRAS wild type tumors ( KRAS mutations in 23.5% of ROS1 RE(+) vs. 49.8% of ROS1 RE(-), p=0.003). Conclusions: ROS1 rearrangements represent rare but clinically actionable molecular driver alterations in MSS CRCs. The detection of ROS1 fusion oncogenes in CRC can pose diagnostic challenges since intrachromosomal ROS1 fusions including GOPC-ROS1 and non-canonical ROS1 fusions such as TTC28-ROS1 can remain negative on fluorescence in situ hybridization and immunohistochemistry assays, respectively. NGS-based comprehensive molecular profiling may be a useful tool to screen for rare fusion oncogenes.

Integrated Analysis Of Immunotherapy Treated Clear Cell Renal Cell Carcinomas: An Exploratory Study

Molecular or immunological differences between responders and nonresponders to immune checkpoint inhibitors (ICIs) of clear cell renal cell carcinomas (ccRCCs) remain incompletely understood. To address this question, we performed next-generation sequencing, methylation analysis, genome wide copy number analysis, targeted RNA sequencing and T-cell receptor sequencing, and we studied frequencies of tumor-infiltrating CD8+ T cells, presence of tertiary lymphoid structures (TLS) and PD-L1 expression in 8 treatment-naive ccRCC patients subsequently treated with ICI (3 responders, 5 nonresponders). Unexpectedly, we identified decreased frequencies of CD8+ tumor-infiltrating T cells and TLS, and a decreased expression of PD-L1 in ICI responders when compared with nonresponders. However, neither tumor-specific genetic alterations nor gene expression profiles correlated with response to ICI or the observed immune features. Our results underline the challenge to stratify ccRCC patients for immunotherapy based on routinely available pathologic primary tumor material, even with advanced technologies. Our findings emphasize the analysis of pretreated metastatic tissue in line with recent observations describing treatment effects on the tumor microenvironment. In addition, our data call for further investigation of additional parameters in a larger ccRCC cohort to understand the mechanistic implications of the observed differences in tumor-infiltrating CD8+ T cells, TLS, and PD-L1 expression.

Modifying the Electron-Trapping Process at the BiVO4 Surface States via the TiO2 Overlayer for Enhanced Water Oxidation

BiVO₄ is one of the most promising photoanode candidates to achieve high-efficiency water splitting. However, overwhelming charge recombination at the interface limits its water oxidation activity. In this study, we show that the water oxidation activity of the BiVO₄ photoanode is significantly boosted by the TiO₂ overlayer prepared by atomic layer deposition. With a TiO₂ overlayer of an optimized thickness, the photocurrent at 1.23 V_RHE increased from 0.64 to 1.1 mA·cm^-2 under front illumination corresponding to 72% enhancement. We attribute this substantial improvement to enhanced charge separation and suppression of surface recombination due to surface-state passivation. We provide direct evidence via transient photocurrent measurements that the TiO₂ overlayer significantly decreases the photogenerated electron-trapping process at the BiVO₄ surface. Electron-trapping passivation leads to enhanced electron photoconductivity, which results in higher photocurrent enhancement under front illumination rather than back illumination. This feature can be particularly useful for wireless tandem devices for water splitting as the higher band gap photoanodes are typically utilized with front illumination in such configurations. Even though the electron-trapping process is eliminated completely at higher TiO₂ overlayer thicknesses, the charge-transfer resistance at the surface also increases significantly, resulting in a diminished photocurrent. We demonstrate that the ultrathin TiO₂ overlayer can be used to fine tune the surface properties of BiVO₄ and may be used for similar purposes for other photoelectrode systems and other photoelectrocatalytic reactions.

Epithelial Wnt secretion drives the progression of inflammation-induced colon carcinoma in murine model

Colon cancer is initiated by stem cells that escape the strict control. This process is often driven through aberrant activation of Wnt signaling by mutations in components acting downstream of the receptor complex that unfetter tumor cells from the need for Wnts. Here we describe a class of colon cancer that does not depend on mutated core components of the Wnt pathway. Genetically blocking Wnt secretion from epithelial cells of such tumors results in apoptosis, reduced expression of colon cancer markers, followed by enhanced tumor differentiation. In contrast to the normal colonic epithelium, such tumor cells autosecrete Wnts to maintain their uncontrolled proliferative behavior. In humans, we determined certain cases of colon cancers in which the Wnt pathway is hyperactive, but not through mutations in its core components. Our findings illuminate the path in therapy to find further subtypes of Wnt-dependent colon cancer that might be responsive to Wnt secretion inhibitors.

•

Acquired expression of epithelial Wnts can drive colon cancer in murine AOM/DSS model

•

Blocking epithelial Wnt-secretion induces apoptosis of AOM/DSS cancer cells

•

The loss of epithelial Wnts promotes differentiation of Wnt-dependent colon tumors

•

Organoids derived from AOM/DSS cancer depend on self-autonomously secreted Wnts

Probing Isoform Switching Events in Various Cancer Types: Lessons From Pan-Cancer Studies

Alternative splicing is an essential regulatory mechanism for gene expression in mammalian cells contributing to protein, cellular, and species diversity. In cancer, alternative splicing is frequently disturbed, leading to changes in the expression of alternatively spliced protein isoforms. Advances in sequencing technologies and analysis methods led to new insights into the extent and functional impact of disturbed alternative splicing events. In this review, we give a brief overview of the molecular mechanisms driving alternative splicing, highlight the function of alternative splicing in healthy tissues and describe how alternative splicing is disrupted in cancer. We summarize current available computational tools for analyzing differential transcript usage, isoform switching events, and the pathogenic impact of cancer-specific splicing events. Finally, the strategies of three recent pan-cancer studies on isoform switching events are compared. Their methodological similarities and discrepancies are highlighted and lessons learned from the comparison are listed. We hope that our assessment will lead to new and more robust methods for cancer-specific transcript detection and help to produce more accurate functional impact predictions of isoform switching events.

An Experimental Methodology to Determine Components of Power Losses of a Gearbox

In this study, an experimental methodology is presented to separate various components of the power loss of a gearbox. The methodology relies on two separate measurements. One is designed to measure total power loss of a gearbox housing a single spur gear pair under both loaded and unloaded conditions such that load-independent (spin) and load-dependent (mechanical) components can be separated. With the assumption that gear pair and rolling element bearings constitute the bulk of the gearbox power loss, a second measurement system designed to quantify rolling element bearing losses is proposed. With this setup, spin and mechanical power losses of rolling element bearings used in the gearbox experiments are measured. Combining the sets of gearbox and bearing data, power loss components attributable to the gear pair and rolling element bearings are quantified as a function of speed and torque. The results indicate that all gear and bearing related components are significant and a methodology such as the one proposed in this study is warranted.

Clinicopathological and Genomic Profiles of Atypical Fibroxanthoma and Pleomorphic Dermal Sarcoma Identify Overlapping Signatures with a High Mutational Burden

Atypical fibroxanthoma (AFX) and pleomorphic dermal sarcoma (PDS) are rare tumors developing in chronically sun-exposed skin. Clinicopathological features are similar, but they differ in prognosis, while PDS has a more aggressive course with a higher risk for local recurrence and metastases. In current clinical practice, they are diagnosed by exclusion using immunohistochemistry. Thus, stringent diagnostic criteria and correct differentiation are critical in management and treatment for optimal outcomes. This retrospective single-center study collected clinicopathological data and tumor samples of 10 AFX and 18 PDS. Extracted genomic DNA from tumor specimens was analyzed by a next-generation sequencing (NGS) platform (FoundationOne-CDx™). Among 65 identified mutations, TP53 inactivating mutations were observed in all tumor specimens. In both AFX and PDS, the known pathogenic gene alterations in CDKN2A, TERT promoter, and NOTCH1 were frequently present, along with high mutational burden and stable Micro-Satellite Instability status. The mutational profiles differed only in ASXL1, which was only present in AFX. Further differences were identified in likely pathogenic and unknown gene alterations. Similarities in their genomic signatures could help to distinguish them from other malignancies, but they are not distinguishable between each other using the FoundationOne-CDx™ NGS panel. Therefore, histological criteria to determine diagnosis remain valid. For further insight, performing deep tumor profiling may be necessary.

Towards advancing scientific knowledge of climate change impacts on short-duration rainfall extremes

A large number of recent studies have aimed at understanding short-duration rainfall extremes, due to their impacts on flash floods, landslides and debris flows and potential for these to worsen with global warming. This has been led in a concerted international effort by the INTENSE Crosscutting Project of the GEWEX (Global Energy and Water Exchanges) Hydroclimatology Panel. Here, we summarize the main findings so far and suggest future directions for research, including: the benefits of convection-permitting climate modelling; towards understanding mechanisms of change; the usefulness of temperature-scaling relations; towards detecting and attributing extreme rainfall change; and the need for international coordination and collaboration. Evidence suggests that the intensity of long-duration (1 day+) heavy precipitation increases with climate warming close to the Clausius-Clapeyron (CC) rate (6-7% K^-1), although large-scale circulation changes affect this response regionally. However, rare events can scale at higher rates, and localized heavy short-duration (hourly and sub-hourly) intensities can respond more strongly (e.g. 2 × CC instead of CC). Day-to-day scaling of short-duration intensities supports a higher scaling, with mechanisms proposed for this related to local-scale dynamics of convective storms, but its relevance to climate change is not clear. Uncertainty in changes to precipitation extremes remains and is influenced by many factors, including large-scale circulation, convective storm dynamics andstratification. Despite this, recent research has increased confidence in both the detectability and understanding of changes in various aspects of intense short-duration rainfall. To make further progress, the international coordination of datasets, model experiments and evaluations will be required, with consistent and standardized comparison methods and metrics, and recommendations are made for these frameworks. This article is part of a discussion meeting issue 'Intensification of short-duration rainfall extremes and implications for flash flood risks'.

Cicer turcicum: A New Cicer Species and Its Potential to Improve Chickpea

Genetic resources of the genus Cicer L. are not only limited when compared to other important food legumes and major cereal crops but also, they include several endemic species with endangered status based on the criteria of the International Union for Conservation of Nature. The chief threats to endemic and endangered Cicer species are over-grazing and habitat change in their natural environments driven by climate changes. During a collection mission in east and south-east Anatolia (Turkey), a new Cicer species was discovered, proposed here as C. turcicum Toker, Berger & Gokturk. Here, we describe the morphological characteristics, images, and ecology of the species, and present preliminary evidence of its potential utility for chickpea improvement. C. turcicum is an annual species, endemic to southeast Anatolia and to date has only been located in a single population distant from any other known annual Cicer species. It belongs to section Cicer M. Pop. of the subgenus Pseudononis M. Pop. of the genus Cicer L. (Fabaceae) and on the basis of internal transcribed spacer (ITS) sequence similarity appears to be a sister species of C. reticulatum Ladiz. and C. echinospermum P.H. Davis, both of which are inter-fertile with domestic chickpea (C. arietinum L.). With the addition of C. turcicum, the genus Cicer now comprises 10 annual and 36 perennial species. As a preliminary evaluation of its potential for chickpea improvement two accessions of C. turcicum were field screened for reproductive heat tolerance and seeds were tested for bruchid resistance alongside a representative group of wild and domestic annual Cicer species. C. turcicum expressed the highest heat tolerance and similar bruchid resistance as C. judaicum Boiss. and C. pinnatifidum Juab. & Spach, neither of which are in the primary genepool of domestic chickpea. Given that C. arietinum and C. reticulatum returned the lowest and the second lowest tolerance and resistance scores, C. turcicum may hold much potential for chickpea improvement if its close relatedness supports interspecific hybridization with the cultigen. Crossing experiments are currently underway to explore this question.

The Fast-Track Water Oxidation Channel on BiVO4 Opened by Nitrogen Treatment

BiVO₄ is one of the most promising photoanode materials for water-splitting systems. Nitrogen incorporation into a BiVO₄ surface overcomes the known bottleneck in its charge-transfer kinetics into the electrolyte. We explored the role of nitrogen in the surface charge recombination and charge-transfer kinetics by employing transient photocurrent spectroscopy at the time scale of surface recombination and water oxidation kinetics, transient absorption spectroscopy, and X-ray photoelectron spectroscopy. We attributed the activity enhancement mechanism to the accelerated V⁵⁺/V⁴⁺ redox process, in which incorporated nitrogen suppresses a limiting surface recombination channel by increasing the oxygen vacancies.

Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network

Under normal conditions, cells of almost all tissue types express the same predominant canonical transcript isoform at each gene locus. In cancer, however, splicing regulation is often disturbed, leading to cancer-specific switches in the most dominant transcripts (MDT). To address the pathogenic impact of these switches, we have analyzed isoform-specific protein-protein interaction disruptions in 1,209 cancer samples covering 27 different cancer types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) project of the International Cancer Genomics Consortium (ICGC). Our study revealed large variations in the number of cancer-specific MDT (cMDT) with the highest frequency in cancers of female reproductive organs. Interestingly, in contrast to the mutational load, cancers arising from the same primary tissue had a similar number of cMDT. Some cMDT were found in 100% of all samples in a cancer type, making them candidates for diagnostic biomarkers. cMDT tend to be located at densely populated network regions where they disrupted protein interactions in the proximity of pathogenic cancer genes. A gene ontology enrichment analysis showed that these disruptions occurred mostly in protein translation and RNA splicing pathways. Interestingly, samples with mutations in the spliceosomal complex tend to have higher number of cMDT, while other transcript expressions correlated with mutations in non-coding splice-site and promoter regions of their genes. This work demonstrates for the first time the large extent of cancer-specific alterations in alternative splicing for 27 different cancer types. It highlights distinct and common patterns of cMDT and suggests novel pathogenic transcripts and markers that induce large network disruptions in cancers.

Fusarium head blight in wheat: contemporary status and molecular approaches

Fusarium head blight (FHB) disease that occurs in wheat is caused by Fusarium graminearum and is a major risk to wheat yield. Although several research efforts focusing on FHB have been conducted in the past several decades, conditions have become more critical due to the increase in its virulent forms. In such a scenario, conferring complete resistance in plants seems to be difficult for handling this issue. The phenotyping for FHB and finding a solution for it at the genetic level comprises a long-term process as FHB infection is largely affected by environmental conditions. Modern molecular strategies have played a crucial role in revealing the host-pathogen interaction in FHB. The integration of molecular biology-based methods such as genome-wide association studies and marker-based genomic selection has provided potential cultivars for breeding programs. In this review, we aim at outlining the contemporary status of the studies conducted on FHB in wheat. The influence of FHB in wheat on animals and human health is also discussed. In addition, a summary of the advancement in the molecular technologies for identifying and developing the FHB-resistant wheat genetic resources is provided. It also suggests the future measures that are required to reduce the world's vulnerability to FHB which was one of the main goals of the US Wheat and Barley Scab Initiative.

Pathway and network analysis of more than 2500 whole cancer genomes

The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding mutations across 2583 whole cancer genomes from 27 tumor types compiled by the ICGC/TCGA PCAWG project that was motivated by the success of pathway and network analyses in prioritizing rare mutations in protein-coding genes. While few non-coding genomic elements are recurrently mutated in this cohort, we identify 93 genes harboring non-coding mutations that cluster into several modules of interacting proteins. Among these are promoter mutations associated with reduced mRNA expression in TP53, TLE4, and TCF4. We find that biological processes had variable proportions of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered primarily by coding mutations, while developmental pathways, including Wnt and Notch, altered by both coding and non-coding mutations. RNA splicing is primarily altered by non-coding mutations in this cohort, and samples containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as samples with coding mutations in these genes. These analyses contribute a new repertoire of possible cancer genes and mechanisms that are altered by non-coding mutations and offer insights into additional cancer vulnerabilities that can be investigated for potential therapeutic treatments.

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

The discovery of drivers of cancer has traditionally focused on protein-coding genes1-4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium5 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers6,7, raise doubts about others and identify novel candidates, including point mutations in the 5' region of TP53, in the 3' untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available.

Tracing Clonal Dynamics Reveals that Two- and Three-dimensional Patient-derived Cell Models Capture Tumor Heterogeneity of Clear Cell Renal Cell Carcinoma

BACKGROUND

Extensive DNA sequencing has led to an unprecedented view of the diversity of individual genomes and their evolution among patients with clear cell renal cell carcinoma (ccRCC).

OBJECTIVE

To understand subclonal architecture and dynamics of patient-derived two-dimensional (2D) and three-dimensional (3D) ccRCC models in vitro, in order to determine whether they mirror ccRCC inter- and intratumor heterogeneity.

DESIGN, SETTING, AND PARTICIPANTS

We have established a comprehensive platform of living renal cancer cell models from ccRCC surgical specimens.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

We confirmed the concordance of 2D and 3D patient-derived cell (PDC) models with the original tumor tissue in terms of histology, biomarker expression, cancer driver mutations, and copy number alterations. We addressed inter- and intrapatient heterogeneity by analyzing clonal dynamics during serial passaging.

RESULTS AND LIMITATIONS

In-depth genetic characterization verified the presence of heterogeneous cell populations, and revealed a high degree of similarity between subclonal compositions of monolayer and organoid cell cultures and the corresponding parental ccRCCs. Clonal dynamics were evident during serial passaging of cells in vitro, suggesting that PDC cultures can offer insights into evolutionary potential and treatment susceptibility of ccRCC subclones in vivo. Proof-of-concept drug profiling using selected ccRCC-targeted therapy agents highlighted patient-specific vulnerabilities in PDC models that could not be anticipated by interrogating commercially available cell lines.

CONCLUSIONS

We demonstrate that PDC models mirror inter- and intratumor heterogeneity of ccRCC in vitro. Based on our findings, we envision that the use of these models will advance our understanding of the trajectories that cause genetic diversity and their consequences for treatment on an individual level.

PATIENT SUMMARY

In this study, we developed two- and three-dimensional patient-derived models from clear cell renal cell carcinoma (ccRCC) as "mini-tumors in a dish." We show that these cell models retain important features of the human ccRCCs such as the profound tumor heterogeneity, thus highlighting their importance for cancer research and precision medicine.

Therapy alteration of solid tumors based on FoundationOne comprehensive genome profiling assay

e14742

Background: Molecular profiling assays are becoming widely available and provide valuable information on tumor characteristics, which can identify targeted therapies or immunotherapies for cancer patients. However, the clinical utility of such tests remains unclear. Within our institution, we analyzed the clinical utility and subsequent treatment alterations of the FoundationOne Comprehensive Genome Profiling Test (FOne). Methods: We conducted a retrospective cohort review (2017 - 2018) of patients with solid tumors under standard diagnostic care who received FOne testing. We reviewed the therapies that were proposed by FOne and studied whether they led to a therapeutic alteration. Results: 71 patients were identified, of which the majority presented a progressive disease state (80%). Among the cancer types most frequently tested were adenocarcinoma of the colon (14%), prostate (8%), lung (4%), intrahepatic cholangiocarcinoma (8%) and breast invasive ductal carcinoma (4%). In 16 cases (22%), therapies suggested by FOne were approved in patient’s tumor type while in 30 cases (42%) therapies were approved in another tumor type. For an additional 13 cases (18%) only therapies tested in clinical trials were reported. 4 patients (6%) received a new therapy based on the FOne result: cancer of unknown primary (Everolimus due to a TSC1 mutation), cutaneous angiosarcoma (Pembrolizumab due to a high tumor mutational burden (TMB)), gastrointestinal neuroendocrine carcinoma (Ipilimumab and Nivolumab due to an intermediate TMB) and mucinous adenocarcinoma of the appendix (Talazoparib due to an ATM mutation). For 11 cases (15%), a new therapy option was identified by FOne, which due to the current treatment plan might be considered for later use. 3 cases (4%) were evaluated for potential clinical trial enrollment. Note that for an additional 6 patients (8%), the therapies proposed by FOne were already established on the basis of previous testing (e.g. smaller genomic panels, IHC, FISH). Conclusions: Overall, 18 (25%) patients received a new therapy option by FOne after standard of care diagnostics. Therapeutic alterations were observed particularly in patients with a rare or unknown tumor type.

Tracking microhabitat temperature variation with iButton data loggers

PREMISE OF THE STUDY

Fine-scale variation in temperature and soil moisture contribute to microhabitats across the landscape, affecting plant phenology, distribution, and fitness. The recent availability of compact and inexpensive temperature and humidity data loggers such as iButtons has facilitated research on microclimates.

METHODS AND RESULTS

Here, we highlight the use of iButtons in three distinct settings: comparisons of empirical data to modeled climate data for rare rock ferns in the genus Asplenium in eastern North America; generation of fine-scale data to predict flowering time and vernalization responsiveness of crop wild relatives of chickpea from southeastern Anatolia; and measurements of extreme thermal variation of solar array installations in Vermont.

DISCUSSION

We highlight a range of challenges with iButtons, including serious limitations of the Hygrochron function that affect their utility for measuring soil moisture, and methods for protecting them from the elements and from human interference. Finally, we provide MATLAB code to facilitate the processing of raw iButton data.

Non-linear regression models for time to flowering in wild chickpea combine genetic and climatic factors

BACKGROUND

Accurate prediction of crop flowering time is required for reaching maximal farm efficiency. Several models developed to accomplish this goal are based on deep knowledge of plant phenology, requiring large investment for every individual crop or new variety. Mathematical modeling can be used to make better use of more shallow data and to extract information from it with higher efficiency. Cultivars of chickpea, Cicer arietanum, are currently being improved by introgressing wild C. reticulatum biodiversity with very different flowering time requirements. More understanding is required for how flowering time will depend on environmental conditions in these cultivars developed by introgression of wild alleles.

RESULTS

We built a novel model for flowering time of wild chickpeas collected at 21 different sites in Turkey and grown in 4 distinct environmental conditions over several different years and seasons. We propose a general approach, in which the analytic forms of dependence of flowering time on climatic parameters, their regression coefficients, and a set of predictors are inferred automatically by stochastic minimization of the deviation of the model output from data. By using a combination of Grammatical Evolution and Differential Evolution Entirely Parallel method, we have identified a model that reflects the influence of effects of day length, temperature, humidity and precipitation and has a coefficient of determination of R2=0.97.

CONCLUSIONS

We used our model to test two important hypotheses. We propose that chickpea phenology may be strongly predicted by accession geographic origin, as well as local environmental conditions at the site of growth. Indeed, the site of origin-by-growth environment interaction accounts for about 14.7% of variation in time period from sowing to flowering. Secondly, as the adaptation to specific environments is blueprinted in genomes, the effects of genes on flowering time may be conditioned on environmental factors. Genotype-by-environment interaction accounts for about 17.2% of overall variation in flowering time. We also identified several genomic markers associated with different reactions to climatic factor changes. Our methodology is general and can be further applied to extend existing crop models, especially when phenological information is limited.

Development of New SSR (Simple Sequence Repeat) Markers for Lentils (Lens culinaris Medik.) from Genomic Library Enriched with AG and AC Microsatellites

Simple sequence repeat (SSR) markers are the major molecular tools for genetic and genomic researches that have been extensively developed and used in major crops. However, few are available for lentils (Lens culinaris M.), economically an important cool-season legume. The lack of informative simple sequence repeat (SSR) markers in lentil has been a major limitation for lentil molecular breeding studies. Therefore, in order to develop SSR markers for lentil, an enriched genomic libraries for AC and AG repeats were constructed from the Lens culinaris cv Kafkas. A total of 350 clones were inquired for the detection of SSRs. Of 350 clones, 68 had SSR motifs. In polymorphism analysis using 53 newly developed SSRs, a total of 144 alleles across 24 lentil cultivars were detected with an average of 4.64 per locus. The average heterozygosity was 0.588 and polymorphism information contents ranged from 0.194 to 0.895 with an average value of 0.520. These newly developed SSRs will constitute useful tools for molecular breeding, mapping, and assessments of genetic diversity and population structure of lentils.

Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation

Domesticated species are impacted in unintended ways during domestication and breeding. Changes in the nature and intensity of selection impart genetic drift, reduce diversity, and increase the frequency of deleterious alleles. Such outcomes constrain our ability to expand the cultivation of crops into environments that differ from those under which domestication occurred. We address this need in chickpea, an important pulse legume, by harnessing the diversity of wild crop relatives. We document an extreme domestication-related genetic bottleneck and decipher the genetic history of wild populations. We provide evidence of ancestral adaptations for seed coat color crypsis, estimate the impact of environment on genetic structure and trait values, and demonstrate variation between wild and cultivated accessions for agronomic properties. A resource of genotyped, association mapping progeny functionally links the wild and cultivated gene pools and is an essential resource chickpea for improvement, while our methods inform collection of other wild crop progenitor species.