A novel strategy for avian species identification by cytochrome b gene

We report a DNA-based test that can be applied to any avian species so that the amplicon can be used in species identification. The need for the test arose from the requirement to enforce the Wildlife Conservation Act in Taiwan where over 150 avian species are protected. It is difficult to enforce the law if no gross morphology is present and hence there is a requirement to develop a DNA test. This study uses a novel strategy for avian species identification by the cytochrome b gene where a series of primer pairs producing amplicons of decreasing size was designed. The test is designed to produce the largest possible amplicon based upon the quality of the DNA in the sample. A total of 331 avian samples were tested representing 40 species. Sequencing of the amplicons revealed limited intraspecies variation and that no DNA sequence was shared by samples from two different avian species. The closest genetic distance among the 40 species was 0.059 which was between Lonchura punctulata and Estrilda melpoda based upon data from the smallest amplicon. A DNA databank including 138 sequence types from 331 samples tested, representing 40 different species, was constructed in this study. A blind test was used to determine the value for this system for forensic applications that successfully identified the species.     

Structural diversity controlled by alkali/alkaline earth metals for heterometallic AeI/AeII-ZnII coordination polymers based on 4-nitrobenzene-1,2-dicarboxylate

Six heterometallic Zn(II) coordination polymers, Zn(H₂O)₃(FNA) (1), [NH₄]₂[Zn(H₂O)₂(FNA)₂] (2), [ZnNa₂(FNA)₂]·3H₂O (3), [ZnK₂(FNA)₂]·H₂O (4), [ZnRb₂(FNA)₂]·2H₂O (5) and [ZnMg(FNA)₂]·4H₂O (6) (H₂FNA = 4-nitrobenzene-1,2-dicarboxylic acid), were synthesised by introducing different alkali/alkaline earth (Ae^I/Ae^II) metals. These complexes exhibit diverse structures with the different Ae^I/Ae^II metals used and distinct ligand coordination modes the ions provide. For 1 and 2, the Zn(II) centres with distorted octahedra are connected by FNA to form 1-D chain structures. The Zn(II) centres in 3–6 with distorted tetrahedra are linked by FNA to form 2-D anionic grid layers. For 3–5, these 2-D anionic grid layers are connected by alkali metal (Na, K and Rb) with the O–Ae^I–O connectivity to exhibit 3-D framework structures, while 6 features a 2-D Zn–Mg network. Luminescence properties of 1–6 have been investigated.     

Allele and haplotype diversity of new multiplex of 19 ChrX‐STR loci in Han population from Guanzhong region (China)

X‐chromosomal short tandem repeats (X‐STRs) have been proved to be useful for some deficiency paternity cases in recent years. Here, we studied the genetic polymorphisms of 19 X‐STR loci (DXS10148‐DXS10135‐DXS8378, DXS10159‐DXS10162‐DXS10164, DXS7132‐DXS10079‐DXS10074‐DXS10075, DXS6809‐DXS6789, DXS7424‐DXS101, DXS10103‐HPRTB‐DXS10101 and DXS7423‐DXS10134) in 252 male and 222 female individuals from Guanzhong Han population, China. No deviation for all 19 loci was observed from the Hardy–Weinberg equilibrium. The polymorphism information content values of the panel of 19 loci were more than 0.5 with the exception of the locus DXS7423. The combined power of discrimination were 0.9999999999999999999994340 in females and 0.9999999999997662 in males, respectively; and the combined mean exclusion chances were 0.999999993764 in duos and 0.999999999997444 in trios, respectively. The haplotype diversities for all the seven clusters of linked loci were more than 0.9. The results showed that the panel of 19 X‐STR loci were powerful for forensic applications in Guanzhong Han population. Locus by locus population comparisons showed significant differences at more than seven loci between Guanzhong Han population and the groups from North America, Europe and Africa.     

Microbiological Study in Petrol-Spiked Soil

The pollution of arable lands and water with petroleum-derived products is still a valid problem, mainly due the extensive works aimed to improve their production technology to reduce fuel consumption and protect engines. An example of the upgraded fuels is the BP 98 unleaded petrol with Active technology. A pot experiment was carried out in which Eutric Cambisol soil was polluted with petrol to determine its effect on the microbiological and biochemical properties of this soil. Analyses were carried out to determine soil microbiome composition—with the incubation and metagenomic methods, the activity of seven enzymes, and cocksfoot effect on hydrocarbon degradation. The following indices were determined: colony development index (CD); ecophysiological diversity index (EP); index of cocksfoot effect on soil microorganisms and enzymes (IF_G); index of petrol effect on soil microorganisms and enzymes (IF_P); index of the resistance of microorganisms, enzymes, and cocksfoot to soil pollution with petrol (RS); Shannon–Weaver’s index of bacterial taxa diversity (H); and Shannon–Weaver’s index of hydrocarbon degradation (ID_H). The soil pollution with petrol was found to increase population numbers of bacteria and fungi, and Protebacteria phylum abundance as well as to decrease the abundance of Actinobacteria and Acidobacteria phyla. The cultivation of cocksfoot on the petrol-polluted soil had an especially beneficial effect mainly on the bacteria belonging to the Ramlibacter, Pseudoxanthomonas, Mycoplana, and Sphingobium genera. The least susceptible to the soil pollution with petrol and cocksfoot cultivation were the bacteria of the following genera: Kaistobacter, Rhodoplanes, Bacillus, Streptomyces, Paenibacillus, Phenylobacterium, and Terracoccus. Cocksfoot proved effective in the phytoremediation of petrol-polluted soil, as it accelerated hydrocarbon degradation and increased the genetic diversity of bacteria. It additionally enhanced the activities of soil enzymes.     

Endophytic Fungal Community of Huperzia serrata: Diversity and Relevance to the Production of Huperzine A by the Plant Host

As the population ages globally, there seem to be more people with Alzheimer’s disease. Unfortunately, there is currently no specific treatment for the disease. At present, Huperzine A (HupA) is one of the best drugs used for the treatment of Alzheimer’s disease and has been used in clinical trials for several years in China. HupA was first separated from Huperzia serrata, a traditional medicinal herb that is used to cure fever, contusions, strains, hematuria, schizophrenia, and snakebite for several hundreds of years in China, and has been confirmed to have acetylcholinesterase inhibitory activity. With the very slow growth of H. serrata, resources are becoming too scarce to meet the need for clinical treatment. Some endophytic fungal strains that produce HupA were isolated from H. serrate in previous studies. In this article, the diversity of the endophytic fungal community within H. serrata was observed and the relevance to the production of HupA by the host plant was further analyzed. A total of 1167 strains were obtained from the leaves of H. serrata followed by the stems (1045) and roots (824). The richness as well as diversity of endophytic fungi within the leaf and stem were higher than in the root. The endophytic fungal community was similar within stems as well as in leaves at all taxonomic levels. The 11 genera (Derxomyces, Lophiostoma, Cyphellophora, Devriesia, Serendipita, Kurtzmanomyces, Mycosphaerella, Conoideocrella, Brevicellicium, Piskurozyma, and Trichomerium) were positively correlated with HupA content. The correlation index of Derxomyces with HupA contents displayed the highest value (CI = 0.92), whereas Trichomerium showed the lowest value (CI = 0.02). Through electrospray ionization mass spectrometry (ESI-MS), it was confirmed that the HS7-1 strain could produce HupA and the total alkaloid concentration was 3.7 ug/g. This study will enable us to screen and isolate the strain that can produce HupA and to figure out the correlation between endophytic fungal diversity with HupA content in different plant organs. This can provide new insights into the screening of strains that can produce HupA more effectively.     

Analysis of 17 Y‐STR loci haplotype and Y‐chromosome haplogroup distribution in five Chinese ethnic groups

To investigate genetic diversity in Chinese populations, 706 unrelated male individuals from five ethnic groups (Han, Korean, Hui, Mongolian, and Tibetan, respectively) were analyzed with 17 Y‐chromosomal STRs. The haplotype diversity was 0.99985 in the combined data. A total of 675 distinct haplotypes were observed, of which 649 were unique. Y‐chromosome haplogroups in the five groups were also predicted with Y‐STR haplotypes. Genetic distance between the five studied ethnic groups and other published groups was analyzed by analysis of molecular variance and visualized in a multidimensional scaling plot. In conclusion, the 17 Y‐STR loci are highly polymorphic markers in the five groups and hence are very useful in forensic application, population genetics, and human evolution studies.     

The Synthesis of Structurally Diverse Macrocycles By Successive Ring Expansion

Structurally diverse macrocycles and medium‐sized rings (9–24 membered scaffolds, 22 examples) can be generated through a telescoped acylation/ring‐expansion sequence, leading to the insertion of linear fragments into cyclic β‐ketoesters without performing a discrete macrocyclization step. The key β‐ketoester motif is regenerated in the ring‐expanded product, meaning that the same sequence of steps can then be repeated (in theory indefinitely) with other linear fragments, allowing macrocycles with precise substitution patterns to be “grown” from smaller rings using the successive ring‐expansion (SuRE) method.     

Multicomponent Reactions,Union of MCRs and Beyond

Multicomponent reactions (MCRs), which are located between one‐ and two‐component and polymerization reactions, provide a number of valuable conceptual and synthetic advantages over stepwise sequential approaches towards complex and valuable molecules. To address current limitations in the number of MCRs and the resulting scaffolds, the concept of union of MCRs was introduced two decades ago by Dömling and Ugi and is rapidly advancing, as is apparent by several recently published works. MCR technology is now widely recognized for its impact on drug discovery projects and is strongly endorsed by industry in addition to academia. Clearly, novel scaffolds accessible in few steps including MCRs will further enhance the field of applications. Additionally, broad expansion of MCR applications in fields such as imaging, materials science, medical devices, agriculture, or futuristic applications in stem cell therapy and theragnostics or solar energy and superconductivity are predicted.     

Recognizing five molecular ligand-binding sites with similar chemical structure

Accurate identification of ligand-binding sites and discovering the protein–ligand interaction mechanism are important for understanding proteins' functions and designing new drugs. Meanwhile, accurate computational prediction and mechanism research are two grand challenges in proteomics. In this article, ligand-binding residues of five ligands (ATP, ADP, GTP, GDP, and NAD) are predicted as a group, due to their similar chemical structures and close biological function relations. The data set of binding sites by five ligands (ATP, ADP, GTP, GDP, and NAD) are collated from Biolip database. Then, five features, containing increment of diversity value, matrix scoring value, auto-covariance, secondary structure information, and surface accessibility information are used in binding site predictions. The support vector machine (SVM) model is used with the five features to predict ligand-binding sites. Finally, prediction results are tested by fivefold cross validation. Accuracy (Acc) of five ligands (ATP, ADP, GTP, GDP, and NAD) achieves 77.4%, 71.2%, 82.1%, 82.9%, and 85.3%, respectively; and Matthew correlation coefficient (MCC) of the above five ligands achieves 0.549, 0.424, 0.643, 0.659, and 0.702, respectively. The research result shows that for ligands with similar chemical structures, microenvironment of their binding sites and their sensitivities to features are similar, while, differences of their ligand-binding properties exist at the same time. © 2019 Wiley Periodicals, Inc.     

Twenty years of exceptional success: The molecular education and research consortium in undergraduate computational chemistry (MERCURY)

The molecular education and research consortium in undergraduate computational chemistry (MERCURY) consortium, established in 2000, has contributed greatly to the scientific development of faculty and undergraduates. The MERCURY faculty peer-reviewed publication rate from 2001 to 2019 of 1.7 papers/faculty/year is 3.4 times the rate of the physical science faculty at primarily undergraduate institutions. We have worked with over 1000 students on research projects since 2001, and 75% of our undergraduate research students have been under-represented in chemistry, either female or students of color. Approximately half of our alumni attend graduate school for the purpose of obtaining advanced degrees in STEM fields, and two-thirds are female and/or students of color. We have had more than 1600 attendees at 18 MERCURY conferences, including 111 invited speakers, 61 of whom have been female and/or faculty of color. In this paper, the research accomplishments, transformational outcomes, and scientific productivity of the MERCURY faculty are highlighted.