Minor Contributor Research Articles

Characterization of Cell Wall Compositions of Sodium Azide-Induced Brittle Mutant Lines in IR64 Variety and Its Potential Application

The rice brittle culm is a cell wall composition changed mutant suitable for studying mechanical strength in rice. However, a thorough investigation of brittle culm has been limited due to the lack of diverse brittle mutants on similar genetic backgrounds in cell walls. In this study, we obtained 45 various brittle mutant lines (BMLs) from the IR64 mutant pool induced by sodium azide mutagenesis using the finger-bending method and texture profile analysis. The first scoring method was established to differentiate the levels of brittleness in rice tissues. The variation of cell wall compositions of BMLs showed that the brittleness in rice primarily correlated with cellulose content supported by high correlation coefficients (R = −0.78) and principal component analysis (PCA = 81.7%). As demonstrated using PCA, lower correlation with brittleness, hemicellulose, lignin, and silica were identified as minor contributors to the overall balance of cell wall compositions and brittleness. The analysis of hydrolysis and feeding indexes highlighted the importance of diversities of brittleness and cell wall compositions of BMLs and their potential applications in ruminant animals and making bioenergy. These results contributed to the comprehension of brittleness and mechanical strength in rice and also extended the applications of rice straw.

The lung is a megakaryocyte outpost that can defend against thrombocytopenic attack.

Lung megakaryocytes (Mks) are a unique subset of Mks that are distinct from their bone marrow counterparts. Recent evidence suggests that lung Mks favor an immune phenotype, but have unclear contributions to the total platelet mass. In this issue of the JCI, Livada et al. used an array of complementary in vivo labeling and tracing models in mice to investigate a longstanding question of where lung Mks are derived. By combining these models with stressed conditions, the authors assessed the contribution of lung Mks to total platelet counts in a homeostatic and thrombocytopenic state. Mks were minor contributors to the circulating pool of platelets during homeostasis but increased output during thrombocytopenia. These findings add critical understanding to the development of lung Mks and demonstrate the dynamic potential of these specialized cells to respond to thrombocytopenia.

Developmental Validation of a DIP-InDel/DIP-STR System for the Detection of Unbalanced DNA Mixtures.

Extracting "masked" minor donor information from an unbalanced DNA mixture stain is important for the identification of the person of interest. In recent years, a series of compound markers genotyped based on allele-specific amplifications have been proposed to detect minor contributors of mixed stains. In this study, we selected out 18 DIP-InDel markers from previous literatures and established a multiplex system encompassing 18 DIP-InDel markers and 6 DIP-STR markers in two separate reactions. The allele frequencies were estimated based on 200 samples, and 23 of the 24 DIP-linked length polymorphic markers had a relatively high probability of informative markers (I value >0.267), which indicated their potential usefulness in the Chinese Han population. Moreover, the multiplex was highly sensitive (requiring >0.025ng) and specific to human DNA. This system is capable of detecting the minor contributor comprising 1% in unbalanced mixtures of two individuals. The capacity of profiling cell-free DNA was also analyzed in few cases. At least one paternal allele could be detected in maternal plasma samples with gestation periods ranging from 27 to 40 weeks. To conclude, the DIP-linked length polymorphic markers may serve as a convenient method for detecting the presence of a minor donor in unbalanced mixtures and show promise for noninvasive prenatal diagnosis.

The role of dissolved organic carbon in Great Smoky Mountains National Park streams impacted by long-term acid deposition.

Following reductions in acid deposition in the Great Smoky Mountains National Park (GRSM) since the 2000s, many streams remain acidic and the role of organic acids (OA-) remains unknown due to limited OA- data. This study investigated dissolved organic carbon (DOC) concentrations as a surrogate for OA- across GRSM and its relationships with watershed characteristics, seasons, flow, and stream chemistry. Baseflow water samples were collected from seven watersheds for 2years and stormflow samples from three watersheds for 1year. During baseflow, DOC concentrations ranged from < 0.04 to 2.29mg L-1 with watershed medians between 0.61 and 1.00mg L-1. Stormflow DOC concentrations ranged from 1.36 to 5.66mg L-1. During the summer, median DOC concentrations were about twice that of the other three seasons. Stream DOC concentrations decreased with increasing elevation during baseflow but increased with increasing elevation during stormflow. Considering high elevations historically received greater acid deposition, this gradient between baseflow and stormflow suggests higher elevation streams are more impacted by OA-. Based on an OA-/DOC acidity model, it was estimated that during baseflow OA- was a minor contributor to stream acidity, in the order of 5.3 μeq L-1, however stormflow OA- was estimated at 52.5 μeq L-1, contributing to nearly half of stream acidity. Baseflow DOC was significantly correlated with pH and Ca2+, suggesting stream acidification/recovery is governed by base cations and Ca2+ availability. Furthermore, this study provides essential data for future research to evaluate stream DOC trends during acidification recovery and changes in biogeochemical processes.

Internal validation of the Precision ID GlobalFiler NGS STR panel v2 kit with locus-specific analytical threshold, and with special regard to mixtures and low template DNA detection

We performed an internal laboratory validation of the Precision ID GlobalFiler NGS STR panel v2 kit to assist the introduction of the technology into the routine forensic casework practice. The study was designed and evaluated based not only on the key validation standards like sensitivity, stability, reproducibility, repeatability, mixture, and concordance, but we also tested the effect of reduced input DNA, we measured and applied locus-specific analytical threshold values, tested two different PCR cycle conditions, sequence artifacts and stutters were also analysed. During the study we also tested the new method on real casework samples. The sensitivity study confirmed that adding 500 pg template DNA for library preparation can be optimal at base PCR cycle number (that was 24), because the measured average heterozygote balance was not lower than 0.82, and each allele was detected above the analytical threshold. However, contrary to previous communications, increasing the PCR cycle numbers up to 28 has not resulted the significant elevation of the heterozygote imbalance. According to our results, raised PCR cycle condition (i.e. 28) is appropriate at or below 150 pg total input DNA. For most loci, the calculated AT was lower than the manufacturer’s recommended. Applying the newly established ATs with raised PCR cycle conditions the allele detection sensitivity and reliability increased. We observed allele dropouts only at the 15 pg template DNA experiments with 5 % frequency, that is better to previously published studies. This result indicates that this low amount of DNA (i.e. 15 pg) could be a minimum limit of template input for a potentially successful analysis. In the mixture study the minor contributor could be detected up to 1:19 mixture ratio. We detected minor alleles in all measurements and concentrations above the threshold if the template DNA were fixed and only SNP differences were observed between the same alleles of the contributors. To test concordance between the new method and traditional STR genotyping we analysed 58 Hungarian individual samples in parallel. Nearby the detected 248 different length-based alleles on the 31 loci in the sample pool we revealed additional 75 sequence variant alleles, that represent an approximately 23 % increase in the total number of observed alleles. The casework study confirmed that the Precision ID GlobalFiler NGS STR panel v2 kit is effective even in genotyping degraded samples with extremely low levels of DNA, if we apply elevated cycle number for library preparation and use locus-specific analytical thresholds.

Applications of Probabilistic Genotyping Method for Combining Evidence Across Microhaplotype DNA Mixture Profiles.

In cases of serious crimes that involve challenging DNA samples from the perpetrator (e.g., a minor contributor to a mixture), there is justification to combine different mixture profiles. In our previous study, we developed a massively parallel sequencing (MPS)-based assay targeting 140 microhaplotype markers. In this study, we extended the use of the microhaplotype panel to common scenarios, such as determining the presence of a common contributor or relatedness between different mixture profiles when no reference source is available. Data interpretation was performed using the R package KinMix. Our findings revealed that correct assignments of a common contributor and relatedness were made between relatively balanced mixtures. However, when profiles suffered from allele imbalance, inclusive assignments were significantly associated with the suspect's mixture proportion. Additionally, our analysis showed zero false-positive rates in the studied scenarios. These results indicate that microhaplotype data can be reliably interpreted for identifying a common donor or related donors among different mixtures. Further research based on larger sample sizes may yield more reliable results, which could assist in solving issues related to complex scenarios where multiple mixed profiles were involved.

Performance comparison of a previously validated microhaplotype panel and a forensic STR panel for DNA mixture analysis

Short Tandem Repeats (STRs) are the most widespread markers in forensic genetics. However, STR stutter peaks can mask alleles from a minor contributor when analysing mixtures, hindering the interpretation of complex profiles. In this study we compared the performance of a previously described panel of microhaplotypes (MHs), an alternative type of forensic marker, against a standard STR kit. The parameters evaluated included: capability of determining the minimum number of contributors in the mixture; percentages of allele drop-outs and drop-ins; retrieval of alleles belonging to the minor contributor, and estimation of likelihood ratio (LR) values. In addition, the capacity of EuroForMix software to estimate each donor’s percentage of contribution was tested, as well as the impact on results when using manually, or automatically prepared libraries. The MH panel showed better performance than STRs for the detection of 2-contributor mixtures, but the lower degree of polymorphism per MH marker hindered the task of deconvolution with multiple contributors. MHs presented higher drop-in rates and lower drop-out rates, a higher capability to recover the minor contributor’s alleles and provided higher LR values than STRs, likely due to the much higher number of loci combined in the panel. Estimations of contributor ratios using EuroForMix showed promising results and marginal differences were found in these values between manually and automatically prepared libraries. Overall, results showed that the mixture detection performance of the MH panel was better or equal to the standard forensic autosomal STR panel, indicating microhaplotypes are informative markers for this purpose.

Transfer and persistence of intruder DNA within an office after reuse by owner

The heightened sensitivity of DNA typing techniques, paired with the extensive use of trace DNA in forensic investigations, has resulted in an increased need to understand how and when DNA is deposited on surfaces of interest. This study focussed on the transfer, persistence, and prevalence of trace DNA in a single occupation of an office space by an intruder, when all contacts made during occupation and for the two hours prior and post occupation were known. The extent to which DNA could be recovered from contacted/not contacted surfaces was investigated. This study investigates the impacts of these movements and use of an office space when the duration of occupancy, surface contact histories and shedder status of participants are known. Contacts were documented and surfaces in the office space were targeted for sampling. Categories were set for target sampling that included different types of contact. Direct and indirect DNA transfer was detected in 55 % and 6 % of samples, respectively. Contactless DNA transfer was detected in 0.5 % of samples. The owner was observed as the sole/major/majority contributor in 77 % of the samples and as minor contributor in 10 % of samples. The intruder was observed as the sole/major/majority contributor in 14 % of samples and as the minor contributor in 16 %. An increased number of contacts increased the relative DNA contribution of the individual making the contact, however, not all observed direct contacts resulted in detectable DNA transfer. The outcome of this study will aid in better sample targeting strategies and contribute to the pool of data assisting in the development of activity level assessments.

Validation of the PowerPlex®35GY System: a novel eight-dye STR multiplex kit on the Spectrum Compact CE System.

The PowerPlex® 35GY System (Promega, USA) is an advanced eight-dye multiplex STR kit, incorporating twenty-three autosomal STR loci, eleven Y chromosome STR loci, one sex determining marker Amelogenin, and two quality indicators. This multiplex system includes 20 CODIS loci and up to 15 mini-STR loci with sizing values less than 250 bases. In this study, validation for PowerPlex® 35GY System was conducted following the guidelines of SWGDAM, encompassing sensitivity, precision, accuracy, concordance, species specificity, stutter, mixture, stability, and degraded DNA. The results from experiments demonstrated that the PowerPlex® 35GY System could effectively amplify DNA samples, with complete allele detection achieved at 125 pg. Moreover, over 90% of alleles from minor contributors were detected at a mixed ratio of 1:4. Additionally, the system was found to yield full profiles even in the presence of hematin, humic acid, and indigo. The PowerPlex® 35GY System demonstrated superior performance in the sensitivity and degraded DNA studies compared to a six-dye STR kit. Hence, it is evident that the PowerPlex® 35GY System is well-suited for forensic practice, whether in casework or for database samples. These findings provide strong support for the efficacy and reliability of the PowerPlex® 35GY System in forensic applications.

Provenance of clay-sized detrital sediments in the North Sea and the Skagerrak region based on radiogenic Nd-Sr-Hf isotopes and clay mineral compositions: assessing the impact of coastal and seabed erosion

The Skagerrak basin represents the main sink area for fine-grained sediment in the North Sea region and constitutes a natural deposition center for sediments that are supplied from the Atlantic, the Baltic Sea and the surrounding continental margins and coasts. However, the exact sources and their proportional contributions to the North Sea sediments and to the Skagerrak deposits are not well understood. To trace the predominant sources of the sediment and to gain a better understanding of the sedimentary processes in the North Sea and the Skagerrak basin, radiogenic Sr, Nd, and Hf isotope signatures and clay mineral compositions of the detrital clay fraction of surface sediment samples from the North Sea, the Scandinavian margins and the Baltic Sea were measured. The results indicate that the major source for Skagerrak clay-size sediments is the northern North Sea but Scandinavia as well as the southern North Sea including the southern England coast also contribute material. Seabed and coastal erosion in the northern North Sea are enhanced by the inflowing Atlantic Currents, which provide the Skagerrak with high amounts of clay size sediments. In contrast, the southern North Sea, the Baltic Sea and mid-European rivers such as Weser, Elbe and Ems are only minor contributors. As Skagerrak deposits are dominated by clay sized material (up to 60%), the reconstructed sediment processes in this study deviate from findings in previous sediment budget studies, which were based on both clay and silt fraction and indicated predominant influences from the southern North Sea. These results highlight that coastal and seabed erosion in the North Sea is a previously underestimated source of fine-grained sediments for depocenters in the entire North Sea. With regard to climate change, the global sea-level rise will likely enhance erosional processes and can therefore significantly influence the sediment budget of the entire North Sea.

Legacy halogenated flame retardants in Canadian human milk from the maternal-infant research on environmental chemicals study

Polybrominated diphenyl ethers (PBDEs) and hexabromocyclododecane (HBCD) were measured in 298 human milk samples collected from across Canada between 2008 and 2011 as part of the Maternal-Infant Research on Environmental Chemicals study. PBDEs were detected in 100% of the samples analyzed and concentrations ranged from 0.071 to 267 ng·g-1 lipid (median 15.6 ng·g-1 lipid). The dominant contributors to ΣPBDEs (Σ15, 17, 28, 37, 47, 66, 71, 75, 77, 85, 99, 100, 119, 138, 153, 154, 160, 183, 190, 209) were PBDE 47 &gt; PBDE 153 &gt; PBDE 99 &gt; PBDE 100 &gt; PBDE 28 &gt; PBDE 209. Previously, PBDE 209 was considered to be a minor contributor to ΣPBDE concentrations in Canadian human milk and, therefore, not reported by our lab. This study showed that when present, PBDE 209 can be an important contributor to ΣPBDEs (range: below detection - 85.3 ng·g-1 lipid; median - 0.083 ng·g-1 lipid). ΣPBDE concentrations declined slightly in Canadian human milk between the early and late 2000s. HBCD (Σ of α-, β-, and γ-) was observed in 94.0% of the samples measured and concentrations were dominated by α-HBCD (93.3%), with β- (9.7%) and γ- (28.5%) less frequently detected. The maximum ΣHBCD concentration observed was 7.66 ng·g-1 lipid (median value 0.303 ng·g-1 lipid). These data suggest that HBCD concentrations similarly decreased in Canadian human milk between the early 2000s and sampling for the present study. Maternal age did not impact the concentrations of these flame retardants in milk. Additionally, other maternal characteristics [e.g., the number of children a woman has had, pre-pregnancy body mass index (BMI), and education level] did not impact concentrations of these brominated flame retardant concentrations.

Application of a newly constructed NGS panel with 45 X-linked microhaplotypes demonstrates the unique value of X-MH for kinship testing and mixture analysis

X-linked microhaplotypes (X-MHs) have the potential to be a valuable supplementary tool in complex kinship identification or the resolution of DNA mixtures, because they bring together the distinctive genetic pattern of X chromosomal markers and the benefits of microhaplotypes (MHs). In this study, we used the 1000 Genome database to screen and select 63 X-MHs; 18 MHs were filtered out though a batch sequencing assessment of the DNA samples collected from 112 unrelated Chinese Han individuals. The resulting 45-plex panel performed well in comprehensive assessments including repeatability, sensitivity, species specificity, resistance to PCR inhibitors or degradation, mutation rate, and accuracy in detecting DNA mixture samples. The minimum amount of DNA template that can be tested with this panel is 0.5 ng. Additionally, the alleles of the minor contributor can be accurately detected when the mixture rate is larger than 1:9 in female-male mixture or 1:19 in male-male mixture. Then, we calculated population parameters on each MH based on the allele frequency data obtained from the sequence results of the aforementioned 112 unrelated samples. Combining these parameters on each MH, it can be calculated that TDPm, TDPf, CPET, CPEDFM, CPEDFF and CNCEP3 of the 45-plex system were 1–8.99×10−13, 1–1.62×10−19, 0.9999999995, 0.9999981, 0.9955, 0.9999971 and 0.99940, respectively, indicating that the panel is capable in personal identification and parentage testing. To reveal the unique advantage of X-MHs in the analyses of complex kinship and male DNA mixture, further assessments were made. For complex kinship identification, 22 types of individual pairs with different second-degree kinship were simulated and different types of likelihood ratios (LR) were calculated for each. The results revealed that the panel can achieve accuracy of approximately 70 %∼80 % when dividing each of the three types of second-degree kinships into three or four groups. Theoretically, such sub-division cannot be done by using independent autosomal markers. For male DNA mixture analysis without suspects, the maximum likelihood ratio strategy was derived and employed in the estimation of the number of male contributors (NOMC). Simulations were conducted to verify the efficacy of the 45-plex panel in the field and to compare it with autosomal markers by assuming the 45 MHs as autosomal ones. The results showed that X-MHs can achieve higher accuracy in the estimation of NOMC than autosomal ones when the mixed males were unrelated. The results highlighted the unique value of X-linked MHs in complex kinship and male mixture analyses.

Improved individual identification in DNA mixtures of unrelated or related contributors through massively parallel sequencing

DNA mixtures are a common sample type in forensic genetics, and we typically assume that contributors to the mixture are unrelated when calculating the likelihood ratio (LR). However, scenarios involving mixtures with related contributors, such as in family murder or incest cases, can also be encountered. Compared to the mixtures with unrelated contributors, the kinship within the mixture would bring additional challenges for the inference of the number of contributors (NOC) and the construction of probabilistic genotyping models. To evaluate the influence of potential kinship on the individual identification of the person of interest (POI), we conducted simulations of two-person (2 P) and three-person (3 P) DNA mixtures containing unrelated or related contributors (parent-child, full-sibling, and uncle-nephew) at different mixing ratios (for 2 P: 1:1, 4:1, 9:1, and 19:1; for 3 P: 1:1:1, 2:1:1, 5:4:1, and 10:5:1), and performed massively parallel sequencing (MPS) using MGIEasy Signature Identification Library Prep Kit on MGI platform. In addition, in silico simulations of mixtures with unrelated and related contributors were also performed. In this study, we evaluated 1): the MPS performance; 2) the influence of multiple genetic markers on determining the presence of related contributors and inferring the NOC within the mixture; 3) the probability distribution of MAC (maximum allele count) and TAC (total allele count) based on in silico mixture profiles; 4) trends in LR values with and without considering kinship in mixtures with related and unrelated contributors; 5) trends in LR values with length- and sequence-based STR genotypes. Results indicated that multiple numbers and types of genetic markers positively influenced kinship and NOC inference in a mixture. The LR values of POI were strongly dependent on the mixing ratio. Non- and correct-kinship hypotheses essentially did not affect the individual identification of the major POI; the correct kinship hypothesis yielded more conservative LR values; the incorrect kinship hypothesis did not necessarily lead to the failure of POI individual identification. However, it is noteworthy that these considerations could lead to uncertain outcomes in the identification of minor contributors. Compared to length-based STR genotyping, using sequence-based STR genotype increases the individual identification power of the POI, concurrently improving the accuracy of mixing ratio inference using EuroForMix. In conclusion, the MGIEasy Signature Identification Library Prep kit demonstrated robust individual identification power, which is a viable MPS panel for forensic DNA mixture interpretations, whether involving unrelated or related contributors.

Tracing the origins of Plasmodium vivax resurgence after malaria elimination on Aneityum Island in Vanuatu

BackgroundFive years after successful malaria elimination, Aneityum Island in Vanuatu experienced an outbreak of Plasmodium vivax of unknown origin in 2002. Epidemiological investigations revealed several potential sources of P. vivax. We aimed to identify the genetic origin of P. vivax responsible for the resurgence.MethodsFive P. vivax microsatellite markers were genotyped using DNA extracted from archived blood samples. A total of 69 samples from four P. vivax populations was included: 29 from the outbreak in 2002, seven from Aneityum in 1999 and 2000, 18 from visitors to Aneityum in 2000, and 15 from nearby Tanna Island in 2002. A neighbour-joining phylogenetic tree was constructed to elucidate the relationships among P. vivax isolates. STRUCTURE and principal component analysis were used to assess patterns of genetic structure.ResultsHere we show distinct genetic origins of P. vivax during the outbreak on Aneityum. While the origin of most P. vivax lineages found during the outbreak remains unidentified, limited genetic diversity among these lineages is consistent with a rapid expansion from a recent common ancestor. Contemporaneous P. vivax from neighboring Tanna and potential relapse of P. vivax acquired from other islands in 1999 and 2000 are also identified as minor contributors to the outbreak.ConclusionsMultiple reintroductions of P. vivax after elimination highlight the high receptivity and vulnerability to malaria resurgence in island settings of Vanuatu, despite robust surveillance and high community compliance to control measures.

Offshore oil and gas infrastructure plays a minor role in marine metapopulation dynamics

Decommissioning consequences of offshore oil and gas infrastructure removal on marine population dynamics, including connectivity, are not well understood. We modelled the connectivity and metapopulation dynamics of three fish and two benthic invertebrate species inhabiting the natural rocky reefs and offshore oil and gas infrastructure located in the Bass Strait, south-east Australia. Using a network approach, we found that platforms are not major sources, destinations, or stepping-stones for most species, yet act as modest sources for connectivity of Corynactis australis (jewel anemone). In contrast, sections of subsea pipelines appear to act as stepping-stones, source and destination habitats of varying strengths for all study species, except for Centrostephanus rodgersii (long-spined sea urchin). Natural reefs were the main stepping-stones, local source, and destination habitats for all study species. These reefs were largely responsible for the overall metapopulation growth of all study species (average of 96 % contribution across all species), with infrastructure acting as a minor contributor (<2 % average contribution). Full or partial decommissioning of platforms should have a very low or negligible impact on the overall metapopulation dynamics of the species explored, except C. australis, while full removal of pipelines could have a low impact on the metapopulation dynamics of benthic invertebrate species and a moderate impact on fish species (up to 34.1 % reduction in the metapopulation growth). We recommend that the decision to remove offshore infrastructure, either in full or in-part, be made on a platform-by-platform basis and consider contributions of pipelines to connectivity and metapopulation dynamics.

Pharmacokinetics and Safety of Atogepant Co-administered with Quinidine Gluconate in Healthy Participants: A Phase 1, Open-Label, Drug-Drug Interaction Study.

Atogepant, an oral calcitonin gene-related peptide receptor antagonist, is approved for the preventive treatment of migraine. Atogepant is a substrate of P-glycoprotein (P-gp), breast cancer resistance protein, organic anion transporting polypeptide transporters, and cytochrome P450 (CYP)3A4 and 2D6. Quinidine is a strong P-gp and CYP2D6 inhibitor. A phase 1 open-label study evaluated the effect of P-gp and CYP2D6 inhibition by quinidine on the pharmacokinetics of atogepant, and the safety and tolerability of atogepant and quinidine gluconate (QG) when co-administered and when given alone in 33 healthy adults. There was no significant change in the atogepant maximum plasma concentration with QG co-administration. The overall systemic exposure, the area under the plasma concentration-time curve (from time 0 to time t or to infinity), of atogepant increased by 25% when co-administered with QG. However, such an increase was not considered clinically relevant. Atogepant did not alter the mean plasma concentration of quinidine at steady state. The incidence of treatment-emergent adverse events (TEAEs) was highest when QG was administered alone (42.4%), which was primarily due to QT prolongation. Most TEAEs reported were mild in severity and resolved within 1-2 days. Co-administration of atogepant with QG did not result in any unexpected tolerability findings in this phase 1 study in healthy participants. The increase in atogepant exposure during QG co-administration could be due to inhibition of CYP2D6 (a minor contributor to atogepant clearance) as well as inhibition of P-gp.

Paleozoic to Mesozoic paleotectonic reconstructions of Gondwana assembly: Insights from petrography, heavy mineral chemistry and detrital U–Th–total Pb monazite geochronology of sandstones in the Pranhita-Godavari Basin (SE India)

The provenance study of Paleo-Mesozoic sediments of the Pranhita-Godavari (P-G) Basin, located in the southeastern India is crucial for the reconstruction of the eastern Gondwanaland, including the India-Antarctica connection. This study examines petrography, heavy mineral chemistry and detrital monazite geochronology of the Permo-Carboniferous to Cretaceous, predominantly fluviatile sandstones in the P-G Basin to track the possible sediment sources in East Antarctica and Eastern India. The sandstones show a gradual shift in composition from feldspatho-quartzose to quartzose arenite from older to younger succession, accompanied by a change in source terranes in a changing setting from transitional continental to the cratonic interior. The heavy minerals of the sandstones are dominated by garnet, rutile, ilmenite, monazite and zircon in order of decreasing abundance. The mineral chemistry of garnet and rutile indicates the predominance of sources from amphibolite to granulite facies rocks with minor inputs from metapelitic sources. The increase in textural and mineralogical maturity of sandstones accompanied by a gradual increase in ilmenite alteration from the bottom to the top of the succession indicates the attainment of tectonic stability with time. U–Th–total Pb dating of detrital monazites yielded three distinct major clusters at (1) 2556–2125 Ma, (2) 969–715 Ma, and (3) 581–418 Ma. Based on the correlation of source composition and monazite geochronology and paleocurrent data, the source of sediments is traced to the orogens of the Eastern Ghats mobile belt, East Antarctica (including Rayner and Napier complex), Karimnagar granulite belt, Khammam schist belt, and Bhopalpatnam granulite belt, situated to the west, south, and southeast of the present outcrops of the P-G Gondwana succession. The younger age populations possibly represent the sediment input from Kuunga Orogen, which represents the youngest orogenic event (635–488 Ma) in the Gondwana assembly. The rocks of Kuunga orogeny, occurring to the south of the basin, was a minor contributor to the P-G Gondwana sediments of this basin. The new data supports that the Eastern Ghats Mobile Belt of India and East Antarctica were conjugate to each other till the Late Triassic Period, both of which contributed major sediments to the P-G Gondwana Basin.

Development and validation of a new multiplex panel using SNaPshot-based DIP-TriSNP markers for forensic DNA mixtures.

Short tandem repeat analysis is challenging when dealing with unbalanced mixtures in forensic cases due to the presence of stutter peaks and large amplicons. In this research, we propose a novel genetic marker called DIP-TriSNP, which combines deletion/insertion polymorphism (DIP) with tri-allelic single nucleotide polymorphism in less than 230bp length of human genome. Based on multiplex PCR and SNaPShot, a panel, including 14 autosomal DIP-TriSNPs and one Y chromosomal DIP-SNP, had been developed and applied to genotyping 102 unrelated Han Chinese individuals in Sichuan of China and simulated a mixture study. The panel sensitivity can reach as low as 0.1ng DNA template, and the minor contributor of DNA can be detected with the highest ratio of 19:1, as indicated by the obtained results. In the Sichuan Han population, the cumulative probability of informative genotypes reached 0.997092, with a combined power of discrimination of 0.999999998801. The panel was estimated to detect more than two alleles in at least one locus in 99.69% of mixtures of the Sichuan Han population. In conclusion, DIP-TriSNPs have shown promising as an innovative DNA marker for identifying the minor contributor in unbalanced DNA mixtures, offering advantages such as short amplifications, increased polymorphism, and heightened sensitivity.

Storability and Brewing Quality of Corn Grits: Impacts of Storage Temperature, Particle Size and Key Compositional Factors

Across international brewing operations corn grits from different suppliers vary substantially in terms of their physical properties and chemical composition. Present research aimed to highlight the key factors determining the brewing quality of stored corn grits. Six grits samples were sourced with different particle sizes (that ranged from 0% to 74% of particles ≤0.355 mm) and stored at 10 °C, 20 °C, or 30 °C for 0, 2, 4, 8, 12, and 16 months. Samples were analysed for moisture, extract, lipid, trihydroxy fatty acids (THFA) and pro-oxidant metal ion contents. Particle size range was measured using sieve analysis. Increasing levels of THFA occurred on storage due to lipid oxidation and are negative indicators of brewing quality. PLS-R modelling of THFA levels (R 2 = 0.83) revealed particle size (hence surface area for oxidation) was the most important factor (∼60% of the total R 2) followed by storage time (∼25%) and temperature (∼7%). Metal ion content and lipid content of grits were minor contributors. Results showed that coarser milling of grits offers protection against lipid oxidation even after 8 months at 30 °C. These insights into key factors determining the rate of lipid oxidation in stored corn grits will help to develop better supply chain management and storage practices with which to assure their brewing quality.

A gold speciation that adds a second layer to synergistic gold-copper toxicity in Cupriavidus metallidurans.

The metal-resistant bacterium Cupriavidus metallidurans occurs in metal-rich environments. In auriferous soils, the bacterium is challenged by a mixture of copper ions and gold complexes, which exert synergistic toxicity. The previously used, self-made Au(III) solution caused a synergistic toxicity of copper and gold that was based on the inhibition of the CupA-mediated efflux of cytoplasmic Cu(I) by Au(I) in this cellular compartment. In this publication, the response of the bacterium to gold and copper was investigated by using a commercially available Au(III) solution instead of the self-made solution. The new solution was five times more toxic than the previously used one. Increased toxicity was accompanied by greater accumulation of gold atoms by the cells. The contribution of copper resistance determinants to the commercially available Au(III) solution and synergistic gold-copper toxicity was studied using single- and multiple-deletion mutants. The commercially available Au(III) solution inhibited periplasmic Cu(I) homeostasis, which is required for the allocation of copper ions to copper-dependent proteins in this compartment. The presence of the gene for the periplasmic Cu(I) and Au(I) oxidase, CopA, decreased the cellular copper and gold content. Transcriptional reporter gene fusions showed that up-regulation of gig, encoding a minor contributor to copper resistance, was strictly glutathione dependent. Glutathione was also required to resist synergistic gold-copper toxicity. The new data indicated a second layer of synergistic copper-gold toxicity caused by the commercial Au(III) solution, inhibition of the periplasmic copper homeostasis in addition to the cytoplasmic one.IMPORTANCEWhen living in auriferous soils, Cupriavidus metallidurans is not only confronted with synergistic toxicity of copper ions and gold complexes but also by different gold species. A previously used gold solution made by using aqua regia resulted in the formation of periplasmic gold nanoparticles, and the cells were protected against gold toxicity by the periplasmic Cu(I) and Au(I) oxidase CopA. To understand the role of different gold species in the environment, another Au(III) solution was commercially acquired. This compound was more toxic due to a higher accumulation of gold atoms by the cells and inhibition of periplasmic Cu(I) homeostasis. Thus, the geo-biochemical conditions might influence Au(III) speciation. The resulting Au(III) species may subsequently interact in different ways with C. metallidurans and its copper homeostasis system in the cytoplasm and periplasm. This study reveals that the geochemical conditions may decide whether bacteria are able to form gold nanoparticles or not.